diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..98059ca --- /dev/null +++ b/.gitignore @@ -0,0 +1,7 @@ +*.pyc +*.c +.snakemake/ +build/ +dist/ +*.egg +*.egg-info diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..223e786 --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2017 MPI for Heart and Lung Research + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..d4a95e6 --- /dev/null +++ b/README.md @@ -0,0 +1,28 @@ +TOBIAS Snakemake pipeline +======================================= + +Introduction +------------ + +ATAC-seq (Assay for Transposase-Accessible Chromatin using high-throughput sequencing) is a sequencing assay for investigating genome-wide chromatin accessibility. The assay applies a Tn5 Transposase to insert sequencing adapters into accessible chromatin, enabling mapping of regulatory regions across the genome. Additionally, the local distribution of Tn5 insertions contains information about transcription factor binding due to the visible depletion of insertions around sites bound by protein - known as _footprints_. + +**TOBIAS** is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data. Please see the [TOBIAS github repository](https://github.molgen.mpg.de/loosolab/TOBIAS/) for details about the individual tools. + +Snakemake how-to: +----------------- + +To use the snakemake pipeline, make sure the included conda environments are installed: +``` +$ conda env create -f environments/tobias.yaml +$ conda env create -f environments/macs.yaml +``` + +You can use the example config (TOBIAS_example.config) or adjust to your own data by replacing the values for each key. Run using: +```bash +$ conda activate TOBIAS_ENV +$ snakemake --configfile example_config.yaml --cores [number of cores] +``` + +Contact +------------ +Mette Bentsen (mette.bentsen (at) mpi-bn.mpg.de) diff --git a/Snakefile b/Snakefile new file mode 100644 index 0000000..fd198d2 --- /dev/null +++ b/Snakefile @@ -0,0 +1,171 @@ +""" +Upper level TOBIAS snake +""" + +import os +import subprocess +import itertools + +#Set config +if workflow.overwrite_configfile != None: + configfile: str(workflow.overwrite_configfile) +else: + configfile: 'TOBIAS.config' +CONFIGFILE = str(workflow.overwrite_configfile) + +#Snake modules used to setup run +include: "snakefiles/helper.snake" + +#shell.prefix("") + +#-------------------------------------------------------------------------------# +#------------------------- CHECK FORMAT OF CONFIG FILE -------------------------# +#-------------------------------------------------------------------------------# + +required = [("data",), + ("run_info",), + ("run_info", "organism"), + ("run_info", "fasta"), + ("run_info", "blacklist"), + ("run_info", "gtf"), + ("run_info", "motifs"), + ("run_info", "output"), + ] + +#Check if all keys are existing and contain information +for key_list in required: + lookup_dict = config + for key in key_list: + try: + lookup_dict = lookup_dict[key] + if lookup_dict == None: + print("ERROR: Missing input for key {0}".format(key_list)) + except: + print("ERROR: Could not find key(s) \"{0}\" in configfile {1}. Please check that your configfile has right format for TOBIAS.".format(":".join(key_list), CONFIGFILE)) + sys.exit() + +#Check if there is at least one condition with bamfiles +if len(config["data"]) > 0: + for condition in config["data"]: + if len(config["data"][condition]) == 0: + print("ERROR: Could not find any bamfiles in \"{0}\" in configfile {1}".format(":".join(("data", condition)), CONFIGFILE)) +else: + print("ERROR: Could not find any conditions (\"data:\{condition\}\") in configfile {0}".format(CONFIGFILE)) + sys.exit() + + +#-------------------------------------------------------------------------------# +#------------------------- WHICH FILES/INFO WERE INPUT? ------------------------# +#-------------------------------------------------------------------------------# + +input_files = [] + +#Files related to experimental data (bam) +CONDITION_IDS = list(config["data"].keys()) +for condition in CONDITION_IDS: + if not isinstance(config["data"][condition], list): + config['data'][condition] = [config['data'][condition]] + input_files.extend(config['data'][condition]) + + +#Flatfiles independent from experimental data (run_info) +FASTA = config['run_info']['fasta'] +BLACKLIST = config['run_info']['blacklist'] +GTF = config['run_info']['gtf'] +OUTPUTDIR = config['run_info']["output"] +BLACKLIST = config['run_info']['blacklist'] +MOTIFDIR = config['run_info']['motifs'] + +input_files.extend([FASTA, BLACKLIST, GTF]) + + +#---------- Test that input files exist -----------# +for file in input_files: + if file != None: + full_path = os.path.abspath(file) + if not os.path.exists(full_path): + exit("ERROR: The following file given in config does not exist: {0}".format(full_path)) + + +#--------------------------------- MOTIFS --------------------------------------# +#Identify IDS of motifs +files = os.listdir(MOTIFDIR) +MOTIF_FILES = {} +for file in files: + full_file = os.path.join(MOTIFDIR, file) + with open(full_file) as f: + for line in f: + if line.startswith("MOTIF"): + columns = line.rstrip().split() + ID = columns[2] + "_" + columns[1] + ID = filafy(ID) + elif line.startswith(">"): + columns = line.replace(">", "").rstrip().split() + ID = columns[1] + "_" + columns[0] + ID = filafy(ID) + MOTIF_FILES[ID] = full_file + +TF_IDS = list(MOTIF_FILES.keys()) + + +#-------------------------------------------------------------------------------# +#------------------------ WHICH FILES SHOULD BE CREATED? -----------------------# +#-------------------------------------------------------------------------------# + +output_files = [] + + +id2bam = {condition:{} for condition in CONDITION_IDS} +for condition in CONDITION_IDS: + config_bams = config['data'][condition] + sampleids = [os.path.splitext(os.path.basename(bam))[0] for bam in config_bams] + id2bam[condition] = {sampleids[i]:config_bams[i] for i in range(len(sampleids))} # Link sample ids to bams + +PLOTNAMES = expand("{condition}_{plotname}", condition=CONDITION_IDS, plotname=["aggregate"]) +if len(CONDITION_IDS) > 1: + PLOTNAMES.extend(["heatmap_comparison", "aggregate_comparison_all", "aggregate_comparison_bound"]) + +output_files.append(expand(os.path.join(OUTPUTDIR, "footprinting", "{condition}_footprints.bw"), condition=CONDITION_IDS)) + +#output_files.append(os.path.join(OUTPUTDIR, "TFBS", "bindetect_results.txt")) +#output_files.append(os.path.join(OUTPUTDIR, "overview", "bindetect_results.txt")) + +#Visualization +output_files.extend(expand(os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots", "{TF}_{plotname}.pdf"), TF=TF_IDS, plotname=PLOTNAMES)) +output_files.extend(expand(os.path.join(OUTPUTDIR, "overview", "all_{plotname}.pdf"), plotname=PLOTNAMES)) + +#Wilson +output_files.extend(expand(os.path.join(OUTPUTDIR, "wilson", "data", "{TF}_overview.clarion"), TF=TF_IDS)) +output_files.append(os.path.join(OUTPUTDIR, "wilson", "HOW_TO_WILSON.txt")) + +#-------------------------------------------------------------------------------# +#------------------------ DEAL WITH SPECIAL ENVIRONMENTS -----------------------# +#-------------------------------------------------------------------------------# + +sys_env = subprocess.check_output(['conda', 'env', 'list'], universal_newlines=True) +env_list = [line.split()[0] for line in sys_env.split("\n") if len(line.split()) > 0] + +# default TOBIAS environment +if "TOBIAS_ENV" not in env_list: + print("Creating TOBIAS environment for the first time") + subprocess.call(["conda", "env", "create", "--file", "environments/tobias.yaml"]) + +# python 2 related envs +if "MACS_ENV" not in env_list: + print("Creating macs environment for the first time") + subprocess.call(["conda", "env", "create", "--file", "environments/macs.yaml"]) + + +#-------------------------------------------------------------------------------# +#---------------------------------- RUN :-) ------------------------------------# +#-------------------------------------------------------------------------------# + +include: "snakefiles/preprocessing.snake" +include: "snakefiles/footprinting.snake" +include: "snakefiles/visualization.snake" +include: "snakefiles/wilson.snake" + +rule all: + input: + output_files + message: "Rule all" diff --git a/data/Bcell_chr4.bam b/data/Bcell_chr4.bam new file mode 100644 index 0000000..d9abf8e Binary files /dev/null and b/data/Bcell_chr4.bam differ diff --git a/data/Bcell_chr4.bam.bai b/data/Bcell_chr4.bam.bai new file mode 100644 index 0000000..e494030 Binary files /dev/null and b/data/Bcell_chr4.bam.bai differ diff --git a/data/Tcell_chr4_1.bam b/data/Tcell_chr4_1.bam new file mode 100644 index 0000000..1ecdcbc Binary files /dev/null and b/data/Tcell_chr4_1.bam differ diff --git a/data/Tcell_chr4_1.bam.bai b/data/Tcell_chr4_1.bam.bai new file mode 100644 index 0000000..2619cec Binary files /dev/null and b/data/Tcell_chr4_1.bam.bai differ diff --git a/data/Tcell_chr4_2.bam b/data/Tcell_chr4_2.bam new file mode 100644 index 0000000..984b40c Binary files /dev/null and b/data/Tcell_chr4_2.bam differ diff --git a/data/Tcell_chr4_2.bam.bai b/data/Tcell_chr4_2.bam.bai new file mode 100644 index 0000000..fb90c2f Binary files /dev/null and b/data/Tcell_chr4_2.bam.bai differ diff --git a/data/blacklist_chr4.bed b/data/blacklist_chr4.bed new file mode 100644 index 0000000..9fbf4ac --- /dev/null +++ b/data/blacklist_chr4.bed @@ -0,0 +1,2 @@ +chr4 49118760 49119010 +chr4 49120790 49121130 diff --git a/data/genes_chr4.gtf b/data/genes_chr4.gtf new file mode 100644 index 0000000..3e06d93 --- /dev/null +++ b/data/genes_chr4.gtf @@ -0,0 +1,2510 @@ +chr4 havana gene 49096 50124 . - . gene_id "ENSG00000248302"; gene_version "3"; gene_name "BNIP3P41"; gene_source "havana"; gene_biotype "transcribed_processed_pseudogene"; +chr4 ensembl_havana gene 53285 88211 . + . gene_id "ENSG00000272602"; gene_version "5"; gene_name "ZNF595"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 105959 107114 . - . gene_id "ENSG00000250238"; gene_version "1"; gene_name "AC253576.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 124480 202303 . + . gene_id "ENSG00000250312"; gene_version "7"; gene_name "ZNF718"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 149738 150317 . + . gene_id "ENSG00000275426"; gene_version "1"; gene_name "AC253576.2"; gene_source "havana"; gene_biotype "sense_intronic"; +chr4 havana gene 201409 205009 . - . gene_id "ENSG00000250892"; gene_version "1"; gene_name "AC108475.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 212610 255985 . + . gene_id "ENSG00000198155"; gene_version "5"; gene_name "ZNF876P"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; +chr4 havana gene 268982 269531 . - . gene_id "ENSG00000251188"; gene_version "1"; gene_name "AC079140.3"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 269866 270175 . - . gene_id "ENSG00000251689"; gene_version "1"; gene_name "AC079140.5"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 270675 305321 . - . gene_id "ENSG00000186777"; gene_version "11"; gene_name "ZNF732"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 336258 336786 . - . gene_id "ENSG00000251535"; gene_version "1"; gene_name "AC079140.4"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 337814 384864 . + . gene_id "ENSG00000131127"; gene_version "13"; gene_name "ZNF141"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 338097 338583 . - . gene_id "ENSG00000248564"; gene_version "1"; gene_name "AC079140.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 342821 342962 . - . gene_id "ENSG00000250321"; gene_version "1"; gene_name "AC079140.2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 mirbase gene 350157 350252 . + . gene_id "ENSG00000207642"; gene_version "1"; gene_name "MIR571"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 havana gene 386174 454070 . + . gene_id "ENSG00000281016"; gene_version "1"; gene_name "AC092574.2"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 393534 393658 . + . gene_id "ENSG00000249025"; gene_version "1"; gene_name "ZNF519P4"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 416118 416537 . - . gene_id "ENSG00000272885"; gene_version "1"; gene_name "AC092574.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 425435 474129 . - . gene_id "ENSG00000251595"; gene_version "7"; gene_name "ABCA11P"; gene_source "havana"; gene_biotype "transcribed_processed_pseudogene"; +chr4 ensembl_havana gene 425815 499156 . - . gene_id "ENSG00000182903"; gene_version "15"; gene_name "ZNF721"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 499210 540196 . + . gene_id "ENSG00000174227"; gene_version "15"; gene_name "PIGG"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 573880 576300 . - . gene_id "ENSG00000273238"; gene_version "2"; gene_name "TMEM271"; gene_source "havana"; gene_biotype "protein_coding"; +chr4 havana gene 577168 584866 . + . gene_id "ENSG00000283183"; gene_version "1"; gene_name "AC116565.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 625584 670782 . + . gene_id "ENSG00000133256"; gene_version "12"; gene_name "PDE6B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 652850 656213 . - . gene_id "ENSG00000242686"; gene_version "4"; gene_name "AC107464.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 661209 661945 . - . gene_id "ENSG00000272927"; gene_version "1"; gene_name "AC107464.3"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 672436 674338 . - . gene_id "ENSG00000169020"; gene_version "9"; gene_name "ATP5ME"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 673580 682033 . + . gene_id "ENSG00000215375"; gene_version "6"; gene_name "MYL5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 681829 689441 . - . gene_id "ENSG00000169026"; gene_version "12"; gene_name "SLC49A3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 705748 770640 . + . gene_id "ENSG00000185619"; gene_version "18"; gene_name "PCGF3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 722275 724034 . - . gene_id "ENSG00000248416"; gene_version "1"; gene_name "AC107464.2"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 757022 757740 . - . gene_id "ENSG00000272588"; gene_version "1"; gene_name "AC139887.4"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 762387 781849 . - . gene_id "ENSG00000249592"; gene_version "5"; gene_name "AC139887.2"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 764487 765074 . - . gene_id "ENSG00000233799"; gene_version "1"; gene_name "AC139887.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 784957 826198 . - . gene_id "ENSG00000168993"; gene_version "14"; gene_name "CPLX1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 836512 837224 . - . gene_id "ENSG00000260262"; gene_version "1"; gene_name "AC139887.3"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 849276 932373 . - . gene_id "ENSG00000178950"; gene_version "16"; gene_name "GAK"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 932387 958656 . + . gene_id "ENSG00000127419"; gene_version "16"; gene_name "TMEM175"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 958887 986895 . - . gene_id "ENSG00000145214"; gene_version "13"; gene_name "DGKQ"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 979073 993440 . - . gene_id "ENSG00000145217"; gene_version "13"; gene_name "SLC26A1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 986997 1004506 . + . gene_id "ENSG00000127415"; gene_version "12"; gene_name "IDUA"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 1009936 1026897 . + . gene_id "ENSG00000127418"; gene_version "14"; gene_name "FGFRL1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 1027678 1028972 . + . gene_id "ENSG00000250259"; gene_version "1"; gene_name "AC019103.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 1056250 1113562 . - . gene_id "ENSG00000178222"; gene_version "12"; gene_name "RNF212"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 1100016 1101558 . - . gene_id "ENSG00000251639"; gene_version "2"; gene_name "AC092535.2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 1113639 1132977 . + . gene_id "ENSG00000251652"; gene_version "1"; gene_name "AC092535.3"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 1115197 1153726 . - . gene_id "ENSG00000215367"; gene_version "10"; gene_name "TMED11P"; gene_source "havana"; gene_biotype "transcribed_unitary_pseudogene"; +chr4 ensembl gene 1118884 1119013 . + . gene_id "ENSG00000212458"; gene_version "1"; gene_name "RF00554"; gene_source "ensembl"; gene_biotype "snoRNA"; +chr4 havana gene 1151372 1153701 . + . gene_id "ENSG00000227189"; gene_version "2"; gene_name "AC092535.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 1166932 1208962 . - . gene_id "ENSG00000159674"; gene_version "11"; gene_name "SPON2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 1167778 1168174 . + . gene_id "ENSG00000273179"; gene_version "1"; gene_name "AC092535.4"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 1210120 1218591 . + . gene_id "ENSG00000280927"; gene_version "1"; gene_name "CTBP1-AS"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 1211448 1249953 . - . gene_id "ENSG00000159692"; gene_version "15"; gene_name "CTBP1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 1249300 1288291 . + . gene_id "ENSG00000196810"; gene_version "4"; gene_name "CTBP1-DT"; gene_source "ensembl_havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 1289851 1340147 . + . gene_id "ENSG00000090316"; gene_version "15"; gene_name "MAEA"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 1347266 1395992 . + . gene_id "ENSG00000163945"; gene_version "16"; gene_name "UVSSA"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 1356581 1358075 . + . gene_id "ENSG00000254094"; gene_version "1"; gene_name "AC078852.2"; gene_source "havana"; gene_biotype "sense_intronic"; +chr4 havana gene 1358479 1359461 . + . gene_id "ENSG00000253399"; gene_version "1"; gene_name "AC078852.1"; gene_source "havana"; gene_biotype "sense_intronic"; +chr4 ensembl_havana gene 1402932 1406331 . - . gene_id "ENSG00000235608"; gene_version "1"; gene_name "NKX1-1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 1550284 1550572 . + . gene_id "ENSG00000272783"; gene_version "1"; gene_name "AC147067.2"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 1574062 1580253 . - . gene_id "ENSG00000244459"; gene_version "2"; gene_name "AC147067.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 1617915 1684302 . - . gene_id "ENSG00000174137"; gene_version "12"; gene_name "FAM53A"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl gene 1683420 1683529 . - . gene_id "ENSG00000207009"; gene_version "1"; gene_name "RF00019"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl_havana gene 1692800 1712555 . - . gene_id "ENSG00000163950"; gene_version "12"; gene_name "SLBP"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 1712821 1713622 . + . gene_id "ENSG00000270195"; gene_version "1"; gene_name "AC016773.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 1715952 1721358 . - . gene_id "ENSG00000168936"; gene_version "10"; gene_name "TMEM129"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 1721490 1745176 . + . gene_id "ENSG00000013810"; gene_version "18"; gene_name "TACC3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 1793293 1808872 . + . gene_id "ENSG00000068078"; gene_version "18"; gene_name "FGFR3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 1811479 1856247 . - . gene_id "ENSG00000168924"; gene_version 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ensembl_havana gene 15002674 15070153 . + . gene_id "ENSG00000137449"; gene_version "15"; gene_name "CPEB2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 15004942 15427914 . - . gene_id "ENSG00000249252"; gene_version "5"; gene_name "AC098829.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl gene 15093767 15094094 . - . gene_id "ENSG00000199420"; gene_version "1"; gene_name "RN7SKP170"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl_havana gene 15339818 15446166 . + . gene_id "ENSG00000163145"; gene_version "12"; gene_name "C1QTNF7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 15358141 15420032 . - . gene_id "ENSG00000251379"; gene_version "1"; gene_name "AC099550.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 15469865 15601557 . + . gene_id "ENSG00000048342"; gene_version "15"; gene_name "CC2D2A"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 15492729 15492972 . - . gene_id "ENSG00000249930"; gene_version "1"; gene_name "AC007016.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 15563698 15564253 . - . gene_id "ENSG00000273133"; gene_version "1"; gene_name "AC116651.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 15604539 15681679 . - . gene_id "ENSG00000118564"; gene_version "14"; gene_name "FBXL5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 15681662 15705565 . + . gene_id "ENSG00000237765"; gene_version "6"; gene_name "FAM200B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 15702950 15738313 . + . gene_id "ENSG00000109743"; gene_version "10"; gene_name "BST1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 15730962 15731627 . - . gene_id "ENSG00000214846"; gene_version "4"; gene_name "AC114744.1"; gene_source 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18021876 . - . gene_id "ENSG00000178177"; gene_version "15"; gene_name "LCORL"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 17911674 17912976 . + . gene_id "ENSG00000235413"; gene_version "3"; gene_name "KRT18P63"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 18488062 18489508 . - . gene_id "ENSG00000251048"; gene_version "1"; gene_name "AC093871.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 19098199 19098740 . + . gene_id "ENSG00000279918"; gene_version "1"; gene_name "AC006840.1"; gene_source "havana"; gene_biotype "TEC"; +chr4 havana gene 19172335 19456994 . - . gene_id "ENSG00000248238"; gene_version "1"; gene_name "LINC02438"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl gene 19181814 19181856 . - . gene_id "ENSG00000251816"; gene_version "1"; gene_name "RNA5SP157"; gene_source "ensembl"; gene_biotype "rRNA_pseudogene"; +chr4 havana gene 19257951 19258337 . - . gene_id 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gene 27223319 27223427 . - . gene_id "ENSG00000222206"; gene_version "1"; gene_name "RF00019"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 havana gene 27262506 27267254 . - . gene_id "ENSG00000251325"; gene_version "1"; gene_name "AC024132.3"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 27585145 27586144 . + . gene_id "ENSG00000250858"; gene_version "1"; gene_name "IGBP1P5"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 27967723 27985063 . - . gene_id "ENSG00000251410"; gene_version "1"; gene_name "AC007106.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 28362279 28402864 . - . gene_id "ENSG00000250038"; gene_version "5"; gene_name "AC109588.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 28435449 28600275 . + . gene_id "ENSG00000250064"; gene_version "1"; gene_name "AC097480.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl gene 28711198 28711476 . + . gene_id 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gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 29962644 29963758 . - . gene_id "ENSG00000244031"; gene_version "3"; gene_name "RPS3AP17"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 30006951 30008316 . - . gene_id "ENSG00000248281"; gene_version "1"; gene_name "AC106868.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 30720415 31146805 . + . gene_id "ENSG00000169851"; gene_version "15"; gene_name "PCDH7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 30776257 30793970 . - . gene_id "ENSG00000249678"; gene_version "1"; gene_name "AC097716.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 30884443 30885182 . - . gene_id "ENSG00000250624"; gene_version "1"; gene_name "MTCYBP43"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 31171144 31211675 . + . gene_id "ENSG00000251182"; gene_version "1"; gene_name 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havana gene 34657606 34669432 . + . gene_id "ENSG00000250597"; gene_version "5"; gene_name "AC093689.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 34714270 34714598 . + . gene_id "ENSG00000275250"; gene_version "1"; gene_name "AC093913.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 34966241 34966344 . - . gene_id "ENSG00000238694"; gene_version "1"; gene_name "RF01210"; gene_source "ensembl"; gene_biotype "snoRNA"; +chr4 havana gene 35487812 35489750 . + . gene_id "ENSG00000250416"; gene_version "2"; gene_name "SEC63P2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 35495898 35496003 . + . gene_id "ENSG00000206665"; gene_version "1"; gene_name "RNU6-573P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 ensembl_havana gene 35948221 36244509 . - . gene_id "ENSG00000047365"; gene_version "11"; gene_name "ARAP2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 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"ENSG00000128040"; gene_version "10"; gene_name "SPINK2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl gene 56810422 56810681 . + . gene_id "ENSG00000278226"; gene_version "1"; gene_name "RF00017"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl gene 56818218 56818314 . - . gene_id "ENSG00000251799"; gene_version "1"; gene_name "RF00019"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl_havana gene 56907876 56966678 . + . gene_id "ENSG00000084093"; gene_version "16"; gene_name "REST"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 56960927 56961373 . - . gene_id "ENSG00000269949"; gene_version "1"; gene_name "AC069307.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 56963370 56978823 . - . gene_id "ENSG00000084092"; gene_version "6"; gene_name "NOA1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 56977722 57031168 . + . gene_id "ENSG00000047315"; gene_version "15"; gene_name "POLR2B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl gene 57002692 57002792 . + . gene_id "ENSG00000251703"; gene_version "1"; gene_name "RNU6-998P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 ensembl_havana gene 57030773 57110385 . - . gene_id "ENSG00000163453"; gene_version "11"; gene_name "IGFBP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 57072683 57073132 . + . gene_id "ENSG00000250384"; gene_version "1"; gene_name "UBE2CP3"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 57109762 57205510 . + . gene_id "ENSG00000245067"; gene_version "6"; gene_name "IGFBP7-AS1"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 57154577 57156452 . + . gene_id "ENSG00000250192"; gene_version "1"; gene_name "AC105390.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 57352999 57353329 . - . gene_id "ENSG00000243920"; gene_version "2"; gene_name "RPS26P24"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 57425872 57465986 . + . gene_id "ENSG00000248505"; gene_version "1"; gene_name "LINC02380"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 57491390 57495233 . + . gene_id "ENSG00000251459"; gene_version "1"; gene_name "AC013724.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 57595940 57605872 . - . gene_id "ENSG00000251049"; gene_version "2"; gene_name "AC107396.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 57605694 57658800 . - . gene_id "ENSG00000250333"; gene_version "1"; gene_name "AC093725.2"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 57720035 57724655 . + . gene_id "ENSG00000249831"; gene_version "2"; gene_name "AC093725.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 58103147 58103434 . + . gene_id "ENSG00000248660"; gene_version "1"; gene_name "SRIP1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 58117758 58118070 . - . gene_id "ENSG00000249105"; gene_version "2"; gene_name "AC096725.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 58524515 58536328 . - . gene_id "ENSG00000250340"; gene_version "1"; gene_name "LINC02494"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 58562165 58565122 . - . gene_id "ENSG00000250078"; gene_version "1"; gene_name "AC019133.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 58780626 58984152 . - . gene_id "ENSG00000251339"; gene_version "5"; gene_name "AC017091.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 58984282 59046959 . + . gene_id "ENSG00000251266"; gene_version "1"; gene_name "LINC02429"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 58987182 58988160 . - . gene_id "ENSG00000249382"; gene_version "2"; gene_name "AC097501.1"; gene_source "havana"; gene_biotype "processed_transcript"; +chr4 havana gene 59047020 59075256 . - . gene_id "ENSG00000250375"; gene_version "2"; gene_name "AC097501.2"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 59152834 59176146 . + . gene_id "ENSG00000249111"; gene_version "1"; gene_name "AC108517.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl gene 59533786 59533898 . + . gene_id "ENSG00000199780"; gene_version "1"; gene_name "RF00019"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 havana gene 59551142 59630324 . - . gene_id "ENSG00000249392"; gene_version "1"; gene_name "AC096588.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 59767816 59792114 . - . gene_id "ENSG00000249892"; gene_version "1"; gene_name "AC093857.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl gene 59833175 59833276 . + . gene_id "ENSG00000201676"; gene_version "1"; gene_name "RF00019"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl gene 59834063 59834167 . + . gene_id "ENSG00000201775"; gene_version "1"; gene_name "RNU6-1325P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 havana gene 60038269 60038586 . + . gene_id "ENSG00000283043"; gene_version "1"; gene_name "AC097655.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 60750586 60789999 . + . gene_id "ENSG00000249066"; gene_version "1"; gene_name "LINC02496"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 60784115 60784696 . + . gene_id "ENSG00000248237"; gene_version "2"; gene_name "AC105420.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 mirbase gene 60922619 60922684 . + . gene_id "ENSG00000265829"; gene_version "1"; gene_name "MIR548AG1"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 havana gene 61143656 61153962 . + . gene_id "ENSG00000240152"; gene_version "2"; gene_name "LINC02271"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 61201258 62078335 . + . gene_id "ENSG00000150471"; gene_version "16"; gene_name "ADGRL3"; gene_source "havana"; gene_biotype "protein_coding"; +chr4 havana gene 61211652 61212203 . + . gene_id "ENSG00000241261"; gene_version "1"; gene_name "RPL17P19"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 61420246 61428221 . - . gene_id "ENSG00000205682"; gene_version "2"; gene_name "AC020741.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 61775449 61775850 . - . gene_id "ENSG00000226439"; gene_version "3"; gene_name "AC108161.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 61906313 61906408 . + . gene_id "ENSG00000202169"; gene_version "1"; gene_name "RF00019"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 havana gene 62071752 62165554 . - . gene_id "ENSG00000248692"; gene_version "5"; gene_name "ADGRL3-AS1"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 62105660 62106049 . - . gene_id "ENSG00000225405"; gene_version "3"; gene_name "RPS15AP17"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 62248294 62248770 . + . gene_id "ENSG00000241344"; gene_version "1"; gene_name "RPL21P47"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 62291562 62292337 . + . gene_id "ENSG00000250249"; gene_version "2"; gene_name "AC105313.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 62489495 62490218 . - . gene_id "ENSG00000248847"; gene_version "2"; gene_name "AC074087.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 62510469 62510771 . + . gene_id "ENSG00000248336"; gene_version "1"; gene_name "HMGN1P11"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 62816826 62818794 . + . gene_id "ENSG00000180673"; gene_version "9"; gene_name "EXOC5P1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 63128311 63143881 . + . gene_id "ENSG00000251055"; gene_version "2"; gene_name "AC097491.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 63350114 63351472 . + . gene_id "ENSG00000231442"; gene_version "3"; gene_name "LARP1BP1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 63468701 63494278 . - . gene_id "ENSG00000250775"; gene_version "1"; gene_name "AC093730.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 64275257 64409468 . - . gene_id "ENSG00000205678"; gene_version "7"; gene_name "TECRL"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl gene 64397694 64397787 . - . gene_id "ENSG00000252104"; gene_version "1"; gene_name "RNU6-191P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 havana gene 64430909 64433215 . + . gene_id "ENSG00000250768"; gene_version "1"; gene_name "DPP3P1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 64606418 64606613 . + . gene_id "ENSG00000251430"; gene_version "1"; gene_name "MTCO3P27"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 64607703 64608831 . - . gene_id "ENSG00000251385"; gene_version "2"; gene_name "MTCYBP16"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 64608905 64609424 . + . gene_id "ENSG00000249893"; gene_version "1"; gene_name "MTND6P16"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 64609454 64610532 . - . gene_id "ENSG00000250169"; gene_version "1"; gene_name "MTND5P13"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 64610616 64610909 . - . gene_id "ENSG00000248259"; gene_version "1"; gene_name "MTND4LP31"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 64610980 64611308 . - . gene_id "ENSG00000249045"; gene_version "1"; gene_name "MTND3P24"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 64611374 64611888 . - . gene_id "ENSG00000248328"; gene_version "1"; gene_name "MTCO3P28"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 64767130 64767897 . - . gene_id "ENSG00000244669"; gene_version "1"; gene_name "AC104689.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 64914281 65024485 . - . gene_id "ENSG00000250125"; gene_version "2"; gene_name "LINC02232"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 65034634 65036017 . - . gene_id "ENSG00000248447"; gene_version "2"; gene_name "AC107058.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 65142703 65145763 . - . gene_id "ENSG00000248998"; gene_version "2"; gene_name "EFL1P2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 65216616 65217433 . + . gene_id "ENSG00000249351"; gene_version "2"; gene_name "AC096754.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 65225867 65241814 . - . gene_id "ENSG00000285711"; gene_version "1"; gene_name "AC018683.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 65319563 65670495 . - . gene_id "ENSG00000145242"; gene_version "13"; gene_name "EPHA5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 65573459 65574328 . + . gene_id "ENSG00000243199"; gene_version "1"; gene_name "AC115223.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 65669961 65698029 . + . gene_id "ENSG00000250846"; gene_version "6"; gene_name "EPHA5-AS1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 65702202 65705553 . + . gene_id "ENSG00000248479"; gene_version "1"; gene_name "AC104137.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl gene 65807240 65807435 . - . gene_id "ENSG00000222765"; gene_version "1"; gene_name "RNU2-40P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 havana gene 65858761 65860204 . + . gene_id "ENSG00000251527"; gene_version "1"; gene_name "AC097110.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 65998846 66150012 . + . gene_id "ENSG00000249413"; gene_version "2"; gene_name "AC116049.2"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 66003281 66016792 . + . gene_id "ENSG00000272304"; gene_version "1"; gene_name "AC096721.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 66094142 66094526 . + . gene_id "ENSG00000236562"; gene_version "4"; gene_name "AC116049.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 mirbase gene 66276824 66276928 . + . gene_id "ENSG00000221563"; gene_version "1"; gene_name "MIR1269A"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 havana gene 66431092 66431521 . + . gene_id "ENSG00000244099"; gene_version "1"; gene_name "RPS23P3"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 66897262 66897371 . + . gene_id "ENSG00000252890"; gene_version "1"; gene_name 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gene_name "TMPRSS11A"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 67991684 68015768 . - . gene_id "ENSG00000229009"; gene_version "7"; gene_name "TMPRSS11GP"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; +chr4 ensembl gene 68003895 68004001 . + . gene_id "ENSG00000207428"; gene_version "1"; gene_name "RNU6-95P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 havana gene 68038544 68039647 . + . gene_id "ENSG00000227725"; gene_version "3"; gene_name "GCOM2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 68049706 68050478 . - . gene_id "ENSG00000283131"; gene_version "1"; gene_name "MTND2P41"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 68053198 68129880 . - . gene_id "ENSG00000198092"; gene_version "5"; gene_name "TMPRSS11F"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 68061822 68063269 . - . gene_id 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68880131 . - . gene_id "ENSG00000251529"; gene_version "1"; gene_name "AC021146.11"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 68883885 68884440 . - . gene_id "ENSG00000248547"; gene_version "2"; gene_name "AC021146.2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 68900651 68900910 . - . gene_id "ENSG00000248613"; gene_version "1"; gene_name "AC021146.3"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 68901008 68906983 . - . gene_id "ENSG00000272626"; gene_version "1"; gene_name "AC021146.12"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 68907918 68908034 . - . gene_id "ENSG00000249985"; gene_version "1"; gene_name "AC021146.6"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 68914928 68924741 . - . gene_id "ENSG00000198277"; gene_version "6"; gene_name "AC021146.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 68928463 68951791 . - . gene_id "ENSG00000135220"; gene_version "10"; gene_name "UGT2A3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 68972999 68975993 . - . gene_id "ENSG00000251498"; gene_version "1"; gene_name "AC021146.10"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 68985009 68988533 . - . gene_id "ENSG00000249735"; gene_version "1"; gene_name "AC021146.5"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 68996935 68997709 . - . gene_id "ENSG00000250277"; gene_version "2"; gene_name "AC021146.7"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 69004862 69020414 . - . gene_id "ENSG00000251685"; gene_version "3"; gene_name "UGT2B27P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 69021656 69022340 . - . gene_id "ENSG00000249890"; gene_version "1"; gene_name "AC107401.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 69027831 69044578 . + . gene_id "ENSG00000250919"; gene_version "1"; gene_name "UGT2B26P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 69051363 69112987 . + . gene_id "ENSG00000171234"; gene_version "13"; gene_name "UGT2B7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 69066395 69069888 . + . gene_id "ENSG00000248763"; gene_version "2"; gene_name "AC111000.2"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 69125274 69126451 . + . gene_id "ENSG00000251284"; gene_version "2"; gene_name "AC111000.5"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 69131351 69134814 . + . gene_id "ENSG00000250100"; gene_version "2"; gene_name "AC111000.3"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 69144734 69147671 . + . gene_id "ENSG00000251427"; gene_version "1"; gene_name 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gene_id "ENSG00000249956"; gene_version "4"; gene_name "UGT2B24P"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 69437357 69441050 . + . gene_id "ENSG00000250828"; gene_version "2"; gene_name "AC108078.3"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 69450014 69451613 . + . gene_id "ENSG00000249686"; gene_version "1"; gene_name "AC108078.2"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 69480165 69526014 . - . gene_id "ENSG00000156096"; gene_version "13"; gene_name "UGT2B4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 69517667 69518400 . - . gene_id "ENSG00000248886"; gene_version "2"; gene_name "UGT2A3P7"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 69572391 69585527 . - . gene_id "ENSG00000251177"; gene_version "2"; gene_name "AC093829.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 69588417 69653249 . - . gene_id "ENSG00000173610"; gene_version "12"; gene_name "UGT2A1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 69589309 69639642 . - . gene_id "ENSG00000271271"; gene_version "5"; gene_name "UGT2A2"; gene_source "havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 69721162 69787961 . - . gene_id "ENSG00000173597"; gene_version "8"; gene_name "SULT1B1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 69791872 69813888 . - . gene_id "ENSG00000236959"; gene_version "1"; gene_name "SULT1D1P"; gene_source "havana"; gene_biotype "transcribed_unitary_pseudogene"; +chr4 havana gene 69810780 69847786 . - . gene_id "ENSG00000284695"; gene_version "1"; gene_name "AC108941.2"; gene_source "havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 69841212 69860152 . - . gene_id "ENSG00000109193"; gene_version "11"; gene_name "SULT1E1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 69888877 69889406 . + . gene_id "ENSG00000251489"; gene_version "2"; gene_name "AC108941.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 69931081 69946574 . + . gene_id "ENSG00000126545"; gene_version "13"; gene_name "CSN1S1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 69955256 69961007 . - . gene_id "ENSG00000135222"; gene_version "6"; gene_name "CSN2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 69995930 70002570 . + . gene_id "ENSG00000126549"; gene_version "9"; gene_name "STATH"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 70028413 70036538 . + . gene_id "ENSG00000205649"; gene_version "7"; gene_name "HTN3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 70050402 70058845 . + . gene_id "ENSG00000126550"; gene_version "8"; gene_name "HTN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 70067386 70085290 . + . gene_id "ENSG00000234124"; gene_version "6"; gene_name "CSN1S2AP"; gene_source "havana"; gene_biotype "transcribed_unitary_pseudogene"; +chr4 ensembl_havana gene 70133616 70176799 . + . gene_id "ENSG00000187533"; gene_version "13"; gene_name "PRR27"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 70196496 70204576 . + . gene_id "ENSG00000109205"; gene_version "16"; gene_name "ODAM"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 70226071 70235252 . + . gene_id "ENSG00000181617"; gene_version "5"; gene_name "FDCSP"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 70242588 70251428 . + . gene_id "ENSG00000171209"; gene_version "3"; gene_name "CSN3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 70334966 70337116 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gene_name "RF00334"; gene_source "ensembl"; gene_biotype "snoRNA"; +chr4 havana gene 73337233 73337771 . - . gene_id "ENSG00000249976"; gene_version "2"; gene_name "AC108157.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 73397114 73421412 . + . gene_id "ENSG00000163631"; gene_version "16"; gene_name "ALB"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 73431138 73456174 . + . gene_id "ENSG00000081051"; gene_version "7"; gene_name "AFP"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 73481683 73504001 . + . gene_id "ENSG00000079557"; gene_version "4"; gene_name "AFM"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 73508803 73534128 . + . gene_id "ENSG00000250436"; gene_version "1"; gene_name "LINC02499"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 73543822 73544013 . + . gene_id "ENSG00000249970"; gene_version "1"; 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88521573 88521789 . - . gene_id "ENSG00000255072"; gene_version "1"; gene_name "PIGY"; gene_source "havana"; gene_biotype "protein_coding"; +chr4 havana gene 88523810 88649847 . + . gene_id "ENSG00000285385"; gene_version "1"; gene_name "AC098582.1"; gene_source "havana"; gene_biotype "protein_coding"; +chr4 havana gene 88523826 88524983 . + . gene_id "ENSG00000285122"; gene_version "1"; gene_name "AC083829.2"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 88527160 88528170 . + . gene_id "ENSG00000249755"; gene_version "2"; gene_name "AC083829.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 88583666 88583972 . - . gene_id "ENSG00000252322"; gene_version "1"; gene_name "RN7SKP244"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl_havana gene 88592423 88708542 . + . gene_id "ENSG00000138641"; gene_version "16"; gene_name "HERC3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl gene 88684848 88684954 . - . gene_id "ENSG00000207524"; gene_version "1"; gene_name "RNU6-33P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 havana gene 88695915 88697829 . - . gene_id "ENSG00000177432"; gene_version "7"; gene_name "NAP1L5"; gene_source "havana"; gene_biotype "protein_coding"; +chr4 havana gene 88709789 88730103 . + . gene_id "ENSG00000248019"; gene_version "2"; gene_name "FAM13A-AS1"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl gene 88710147 88710265 . + . gene_id "ENSG00000278151"; gene_version "1"; gene_name "RF02114"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl gene 88723209 88723316 . + . gene_id "ENSG00000276003"; gene_version "1"; gene_name "RF02115"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl_havana gene 88725955 89111398 . - . gene_id "ENSG00000138640"; gene_version "14"; gene_name "FAM13A"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 89111500 89114899 . + . gene_id 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gene_name "RNA5SP164"; gene_source "ensembl"; gene_biotype "rRNA_pseudogene"; +chr4 ensembl_havana gene 93828753 93830964 . + . gene_id "ENSG00000172238"; gene_version "4"; gene_name "ATOH1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 94117792 94207556 . - . gene_id "ENSG00000246541"; gene_version "2"; gene_name "AC096746.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 94195940 94196513 . - . gene_id "ENSG00000250897"; gene_version "2"; gene_name "HMGB3P15"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 94207611 94291292 . + . gene_id "ENSG00000163104"; gene_version "17"; gene_name "SMARCAD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 94298535 94342876 . - . gene_id "ENSG00000163106"; gene_version "10"; gene_name "HPGDS"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 94369833 94370163 . + . gene_id 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gene_name "RN7SL275P"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 havana gene 110146374 110147248 . + . gene_id "ENSG00000248200"; gene_version "2"; gene_name "AC093770.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 110251871 110252099 . - . gene_id "ENSG00000166530"; gene_version "8"; gene_name "HSBP1P2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 110264865 110265017 . - . gene_id "ENSG00000250594"; gene_version "2"; gene_name "AC108145.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 110278185 110278291 . + . gene_id "ENSG00000212160"; gene_version "1"; gene_name "RNU6-205P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 havana gene 110291644 110293573 . + . gene_id "ENSG00000250304"; gene_version "2"; gene_name "ZBED1P1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 110365733 110565285 . + . gene_id "ENSG00000138792"; gene_version "9"; gene_name "ENPEP"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 110399773 110400511 . - . gene_id "ENSG00000251464"; gene_version "2"; gene_name "RPL7L1P13"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 110415898 110418504 . + . gene_id "ENSG00000251046"; gene_version "2"; gene_name "ZNF969P"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 110433109 110433188 . - . gene_id "ENSG00000199894"; gene_version "1"; gene_name "RF00494"; gene_source "ensembl"; gene_biotype "snoRNA"; +chr4 havana gene 110512488 110519505 . - . gene_id "ENSG00000250511"; gene_version "1"; gene_name "AC098798.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 110595513 110615458 . - . gene_id "ENSG00000250103"; gene_version "2"; gene_name "PANCR"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 110617423 110642123 . - . gene_id "ENSG00000164093"; gene_version "16"; gene_name "PITX2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 110794403 110797344 . + . gene_id "ENSG00000249519"; gene_version "1"; gene_name "LINC01438"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 mirbase gene 110860582 110860647 . - . gene_id "ENSG00000215961"; gene_version "1"; gene_name "MIR297"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 havana gene 110945109 110945799 . - . gene_id "ENSG00000251483"; gene_version "2"; gene_name "LYPLA1P2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 111063583 111064227 . + . gene_id "ENSG00000251312"; gene_version "2"; gene_name "AC004062.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 111331412 111331518 . + . gene_id "ENSG00000200963"; gene_version "1"; gene_name "RNU6-289P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 havana gene 111551854 111552173 . + . gene_id "ENSG00000241722"; gene_version "2"; gene_name "AC083795.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 111640495 111648808 . + . gene_id "ENSG00000248656"; gene_version "1"; gene_name "AC083795.2"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 111802801 111839886 . + . gene_id "ENSG00000250855"; gene_version "1"; gene_name "AC139718.2"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 111804418 111809694 . - . gene_id "ENSG00000248432"; gene_version "1"; gene_name "AC139718.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 111826881 112072698 . - . gene_id "ENSG00000249815"; gene_version "1"; gene_name "AC004704.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 112068010 112068526 . + . gene_id "ENSG00000250556"; gene_version "1"; gene_name "CCDC34P1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 112077598 112078400 . + . gene_id "ENSG00000250307"; gene_version "2"; gene_name "TUBB8P3"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 112116510 112116903 . - . gene_id "ENSG00000240459"; gene_version "2"; gene_name "AC093663.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 112145397 112195256 . + . gene_id "ENSG00000174749"; gene_version "5"; gene_name "FAM241A"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 112171215 112171527 . + . gene_id "ENSG00000243280"; gene_version "2"; gene_name "AC093663.2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 112229561 112231596 . - . gene_id "ENSG00000260526"; gene_version "1"; gene_name "AC109347.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 112231737 112270047 . + . gene_id "ENSG00000138660"; gene_version "11"; gene_name "AP1AR"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 112272968 112273316 . - . gene_id "ENSG00000272567"; gene_version "1"; gene_name "AC109347.2"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 112274542 112285903 . - . gene_id "ENSG00000145365"; gene_version "10"; gene_name "TIFA"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 112285509 112442620 . + . gene_id "ENSG00000073331"; gene_version "17"; gene_name "ALPK1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 112356135 112359819 . + . gene_id "ENSG00000251441"; gene_version "2"; gene_name "RTEL1P1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 112455924 112457785 . + . gene_id "ENSG00000248697"; gene_version "1"; gene_name "TOX4P1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 112513516 112516172 . - . gene_id "ENSG00000178403"; gene_version "3"; gene_name "NEUROG2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 112515385 112546881 . + . gene_id "ENSG00000249509"; gene_version "1"; gene_name "AC023886.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 112530371 112530672 . - . gene_id "ENSG00000248439"; gene_version "2"; gene_name "RPL23AP94"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 112539333 112636995 . - . gene_id "ENSG00000138658"; gene_version "15"; gene_name "ZGRF1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 112564988 112565398 . + . gene_id "ENSG00000250966"; gene_version "2"; gene_name "AC023886.2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 112636964 112657592 . + . gene_id "ENSG00000174720"; gene_version "15"; gene_name "LARP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 112646476 112650051 . - . gene_id "ENSG00000249532"; gene_version "5"; gene_name "AC106864.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 mirbase gene 112647874 112647941 . - . gene_id "ENSG00000199169"; gene_version "1"; gene_name "MIR367"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 mirbase gene 112648004 112648071 . - . gene_id "ENSG00000199145"; gene_version "1"; gene_name "MIR302D"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 mirbase gene 112648183 112648251 . - . gene_id "ENSG00000207927"; gene_version "1"; gene_name "MIR302A"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 mirbase gene 112648363 112648430 . - . gene_id "ENSG00000199102"; gene_version "1"; gene_name "MIR302C"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 mirbase gene 112648485 112648557 . - . gene_id "ENSG00000284463"; gene_version "1"; gene_name "MIR302B"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 havana gene 112685055 112685503 . + . gene_id "ENSG00000220924"; gene_version "4"; gene_name "OSTCP4"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 112693047 112706810 . - . gene_id "ENSG00000250046"; gene_version "3"; gene_name "AC106864.2"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 112693459 112693792 . - . gene_id "ENSG00000248633"; gene_version "1"; gene_name "WRBP1"; gene_source "havana"; gene_biotype "transcribed_processed_pseudogene"; +chr4 havana gene 112738672 112739106 . + . gene_id "ENSG00000241002"; gene_version "1"; gene_name "AC017007.3"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 112755816 112755917 . - . gene_id "ENSG00000202536"; gene_version "2"; gene_name "RF00019"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 havana gene 112788083 112788878 . - . gene_id "ENSG00000241741"; gene_version "1"; gene_name "RPL7AP30"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 112797050 112798691 . - . gene_id "ENSG00000250500"; gene_version "1"; gene_name "AC017007.4"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 112818109 113383740 . + . gene_id "ENSG00000145362"; gene_version "17"; gene_name "ANK2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 112826307 112827607 . + . gene_id "ENSG00000234841"; gene_version "4"; gene_name "AC017007.2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 112880298 112882330 . - . gene_id "ENSG00000251126"; gene_version "2"; gene_name "AC017007.5"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 112881718 112882132 . - . gene_id "ENSG00000228814"; gene_version "4"; gene_name "AC017007.1"; gene_source "havana"; gene_biotype "transcribed_processed_pseudogene"; +chr4 havana gene 112979590 113071962 . - . gene_id "ENSG00000248152"; gene_version "1"; gene_name "AC093879.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 113031287 113034551 . - . gene_id "ENSG00000249373"; gene_version "2"; gene_name "AC093879.2"; gene_source "havana"; gene_biotype "antisense"; +chr4 mirbase gene 113106863 113106955 . + . gene_id "ENSG00000283193"; gene_version "1"; gene_name "MIR1243"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 mirbase gene 113152282 113152362 . + . gene_id "ENSG00000275810"; gene_version "1"; gene_name "MIR8082"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 havana gene 113214046 113217170 . - . gene_id "ENSG00000196656"; gene_version "7"; gene_name "AC004057.1"; gene_source "havana"; gene_biotype "transcribed_processed_pseudogene"; +chr4 ensembl gene 113419840 113420136 . + . gene_id "ENSG00000239279"; gene_version "3"; gene_name "RN7SL184P"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl gene 113420323 113420486 . + . gene_id "ENSG00000206820"; gene_version "1"; gene_name "RNU1-138P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 ensembl_havana gene 113451032 113761927 . - . gene_id "ENSG00000145349"; gene_version "16"; gene_name "CAMK2D"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 113840050 113840236 . + . gene_id "ENSG00000250229"; gene_version "1"; gene_name "AC111193.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 113900284 113979727 . - . gene_id "ENSG00000180801"; gene_version "13"; gene_name "ARSJ"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 113943256 113944320 . + . gene_id "ENSG00000249304"; gene_version "1"; gene_name "AC104779.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 114103938 114104225 . + . gene_id "ENSG00000248716"; gene_version "2"; gene_name "AC093815.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 114598455 114678224 . + . gene_id "ENSG00000174607"; gene_version "10"; gene_name "UGT8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 mirbase gene 114656759 114656854 . + . gene_id "ENSG00000207931"; gene_version "1"; gene_name "MIR577"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 havana gene 114713579 114714920 . - . gene_id "ENSG00000250215"; gene_version "1"; gene_name "CIR1P2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 114799331 114799629 . + . gene_id "ENSG00000240637"; gene_version "3"; gene_name "RN7SL808P"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl_havana gene 114827763 115113876 . - . gene_id "ENSG00000138653"; gene_version "9"; gene_name "NDST4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 115142982 115143303 . + . gene_id "ENSG00000251308"; gene_version "1"; gene_name "MRPS33P3"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 115628812 115629707 . + . gene_id "ENSG00000250693"; gene_version "2"; gene_name "RPF2P2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 115764099 115764819 . - . gene_id "ENSG00000248488"; gene_version "2"; gene_name "PGAM4P2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 115920707 115921978 . + . gene_id "ENSG00000250363"; gene_version "1"; gene_name "KRT18P21"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 115922015 116297160 . - . gene_id "ENSG00000249259"; gene_version "3"; gene_name "AC027613.1"; gene_source "havana"; gene_biotype "transcribed_processed_pseudogene"; +chr4 havana gene 116043407 116044045 . - . gene_id "ENSG00000250442"; gene_version "1"; gene_name "EIF3KP3"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 116193997 116194751 . - . gene_id "ENSG00000250627"; gene_version "2"; gene_name "TTC39CP1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 116298876 116300320 . + . gene_id "ENSG00000270394"; gene_version "4"; gene_name "MTRNR2L13"; gene_source "havana"; gene_biotype "protein_coding"; +chr4 mirbase gene 116299725 116299768 . + . gene_id "ENSG00000284253"; gene_version "1"; gene_name "MIR1973"; gene_source "mirbase"; gene_biotype "miRNA"; 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gene_version "10"; gene_name "SYNPO2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 119006032 119006401 . + . gene_id "ENSG00000249002"; gene_version "2"; gene_name "AC096745.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 119042024 119043937 . + . gene_id "ENSG00000280551"; gene_version "1"; gene_name "AC096745.2"; gene_source "havana"; gene_biotype "TEC"; +chr4 ensembl_havana gene 119135784 119187789 . + . gene_id "ENSG00000172399"; gene_version "5"; gene_name "MYOZ2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 119192773 119212644 . - . gene_id "ENSG00000178636"; gene_version "8"; gene_name "AC092656.1"; gene_source "havana"; gene_biotype "transcribed_processed_pseudogene"; +chr4 ensembl_havana gene 119212587 119295517 . + . gene_id "ENSG00000145390"; gene_version "11"; gene_name "USP53"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 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gene_name "ANXA5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 121758930 121765427 . - . gene_id "ENSG00000164112"; gene_version "13"; gene_name "TMEM155"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 121764585 121766814 . + . gene_id "ENSG00000226757"; gene_version "2"; gene_name "PP12613"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 121801317 121817021 . + . gene_id "ENSG00000123737"; gene_version "12"; gene_name "EXOSC9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 121816444 121823933 . - . gene_id "ENSG00000145386"; gene_version "9"; gene_name "CCNA2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 121824440 121870497 . - . gene_id "ENSG00000138686"; gene_version "9"; gene_name "BBS7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 121870583 121872848 . + . gene_id "ENSG00000261501"; gene_version "1"; gene_name "AC079341.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 121879027 121951754 . - . gene_id "ENSG00000138741"; gene_version "10"; gene_name "TRPC3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 122077840 122078318 . - . gene_id "ENSG00000237868"; gene_version "1"; gene_name "AC097533.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 122087508 122087811 . - . gene_id "ENSG00000241037"; gene_version "3"; gene_name "RN7SL335P"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl_havana gene 122152333 122362758 . + . gene_id "ENSG00000138688"; gene_version "15"; gene_name "KIAA1109"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 122378966 122429802 . + . gene_id "ENSG00000164113"; gene_version "10"; gene_name "ADAD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 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gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 142023160 142847432 . - . gene_id "ENSG00000109452"; gene_version "12"; gene_name "INPP4B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 142286917 142287625 . - . gene_id "ENSG00000242134"; gene_version "2"; gene_name "RPL5P13"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 142317238 142317546 . + . gene_id "ENSG00000250835"; gene_version "1"; gene_name "LSM3P4"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 142514446 142518983 . + . gene_id "ENSG00000251248"; gene_version "1"; gene_name "AC139720.2"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 142566019 142660950 . + . gene_id "ENSG00000249806"; gene_version "1"; gene_name "AC139720.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 142933195 143184861 . - . gene_id "ENSG00000250326"; gene_version "1"; gene_name 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gene_name "MIR3139"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 havana gene 143349275 143350117 . - . gene_id "ENSG00000228981"; gene_version "3"; gene_name "AC097658.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 143424753 143426013 . + . gene_id "ENSG00000243175"; gene_version "1"; gene_name "RPSAP36"; gene_source "havana"; gene_biotype "transcribed_processed_pseudogene"; +chr4 havana gene 143497412 143498126 . - . gene_id "ENSG00000250540"; gene_version "1"; gene_name "AC104685.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 143513463 143557486 . + . gene_id "ENSG00000153147"; gene_version "5"; gene_name "SMARCA5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 143513472 143514635 . - . gene_id "ENSG00000245112"; gene_version "2"; gene_name "SMARCA5-AS1"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 143555082 143555583 . - . gene_id "ENSG00000248924"; gene_version "2"; gene_name "AC139713.1"; gene_source "havana"; gene_biotype "transcribed_processed_pseudogene"; +chr4 havana gene 143559457 144188367 . + . gene_id "ENSG00000251600"; gene_version "6"; gene_name "AC139713.2"; gene_source "havana"; gene_biotype "processed_transcript"; +chr4 havana gene 143559472 143561460 . + . gene_id "ENSG00000236296"; gene_version "8"; gene_name "GUSBP5"; gene_source "havana"; gene_biotype "transcribed_processed_pseudogene"; +chr4 ensembl_havana gene 143577302 143700675 . - . gene_id "ENSG00000183090"; gene_version "5"; gene_name "FREM3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 143760399 143762093 . - . gene_id "ENSG00000250345"; gene_version "2"; gene_name "AC104090.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 143870867 143905563 . - . gene_id "ENSG00000197465"; gene_version "13"; gene_name "GYPE"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 143911514 143912053 . - . gene_id "ENSG00000249741"; gene_version "2"; gene_name "AC093890.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 143996104 144019345 . - . gene_id "ENSG00000250361"; gene_version "8"; gene_name "GYPB"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 144109303 144140786 . - . gene_id "ENSG00000170180"; gene_version "21"; gene_name "GYPA"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 144111039 144870953 . - . gene_id "ENSG00000285783"; gene_version "1"; gene_name "AC098588.2"; gene_source "havana"; gene_biotype "processed_transcript"; +chr4 havana gene 144210701 145098174 . - . gene_id "ENSG00000285713"; gene_version "1"; gene_name "AC098588.1"; gene_source "havana"; gene_biotype "protein_coding"; +chr4 havana gene 144505900 144509001 . + . gene_id "ENSG00000261129"; gene_version "1"; gene_name "AC106871.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 144572238 144572983 . + . gene_id "ENSG00000250504"; gene_version "2"; gene_name "KRT18P51"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 144642922 144661357 . - . gene_id "ENSG00000248890"; gene_version "1"; gene_name "HHIP-AS1"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 144646021 144745271 . + . gene_id "ENSG00000164161"; gene_version "9"; gene_name "HHIP"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl gene 144739762 144739941 . - . gene_id "ENSG00000273621"; gene_version "1"; gene_name "RF02271"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl_havana gene 144831908 145098541 . - . gene_id "ENSG00000164162"; gene_version "13"; gene_name "ANAPC10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 144845625 144847344 . + . gene_id "ENSG00000249193"; gene_version "1"; gene_name "HSPD1P5"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 144851572 144874787 . + . gene_id "ENSG00000250406"; gene_version "1"; gene_name "AC109811.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 144920713 144921164 . - . gene_id "ENSG00000251452"; gene_version "2"; gene_name "AC109811.2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 145035132 145035436 . + . gene_id "ENSG00000222594"; gene_version "1"; gene_name "RN7SKP235"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 ensembl_havana gene 145097932 145129179 . + . gene_id "ENSG00000164163"; gene_version "10"; gene_name "ABCE1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 145110838 145180161 . - . gene_id "ENSG00000164164"; gene_version "16"; gene_name "OTUD4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl gene 145149537 145149649 . - . gene_id "ENSG00000238713"; gene_version "1"; gene_name "RF00019"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 havana gene 145269810 145270558 . - . gene_id "ENSG00000240992"; gene_version "1"; gene_name "RPS23P4"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 145335263 145340421 . - . gene_id "ENSG00000272727"; gene_version "1"; gene_name "LINC02266"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 145375543 145376253 . + . gene_id "ENSG00000251333"; gene_version "3"; gene_name "RTN3P1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 145376909 145377957 . + . gene_id "ENSG00000278943"; gene_version "1"; gene_name "AC079228.1"; gene_source "havana"; gene_biotype "TEC"; +chr4 havana gene 145456005 145456844 . + . gene_id "ENSG00000248745"; gene_version "2"; gene_name "NMNAT1P4"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 145481194 145558079 . + . gene_id "ENSG00000170365"; gene_version "9"; gene_name "SMAD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 145497073 145502971 . - . gene_id "ENSG00000250582"; gene_version "1"; gene_name "SMAD1-AS2"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 145514615 145517118 . - . gene_id "ENSG00000250902"; gene_version "1"; gene_name "SMAD1-AS1"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 145599042 145660035 . + . gene_id "ENSG00000151611"; gene_version "14"; gene_name "MMAA"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 145624159 145626035 . - . gene_id "ENSG00000249245"; gene_version "2"; gene_name "NCOA4P3"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 145642336 145650624 . - . gene_id "ENSG00000248356"; gene_version "1"; gene_name "AC093864.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl_havana gene 145680115 145771032 . + . gene_id "ENSG00000237136"; gene_version "7"; gene_name "C4orf51"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 145757627 145938635 . - . gene_id "ENSG00000151612"; gene_version "15"; gene_name "ZNF827"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 145830456 145832980 . - . gene_id "ENSG00000279481"; gene_version "1"; gene_name "AC104791.2"; gene_source "havana"; gene_biotype "TEC"; +chr4 havana gene 145833118 145839580 . + . gene_id "ENSG00000251687"; gene_version "1"; gene_name "AC104791.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 ensembl gene 145958128 145958240 . - . gene_id "ENSG00000201314"; gene_version "1"; gene_name "RF00019"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 havana gene 146052604 146056762 . - . gene_id "ENSG00000260303"; gene_version "1"; gene_name "AC108206.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 146077846 146108157 . - . gene_id "ENSG00000251024"; gene_version "1"; gene_name 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gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 146957438 146975457 . + . gene_id "ENSG00000248346"; gene_version "1"; gene_name "AC092435.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 147005492 147009145 . + . gene_id "ENSG00000260090"; gene_version "1"; gene_name "AC092435.3"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 147025914 147030072 . + . gene_id "ENSG00000279376"; gene_version "1"; gene_name "AC092435.4"; gene_source "havana"; gene_biotype "TEC"; +chr4 mirbase gene 147344629 147344717 . - . gene_id "ENSG00000221369"; gene_version "1"; gene_name "MIR548G"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 havana gene 147425974 147426351 . - . gene_id "ENSG00000241281"; gene_version "1"; gene_name "AC010683.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 147458724 147459321 . - . gene_id "ENSG00000249004"; gene_version "1"; gene_name "PRMT5P1"; gene_source "havana"; gene_biotype 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gene_biotype "protein_coding"; +chr4 ensembl_havana gene 147637785 147684230 . - . gene_id "ENSG00000164169"; gene_version "12"; gene_name "PRMT9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 147732063 148072780 . + . gene_id "ENSG00000071205"; gene_version "11"; gene_name "ARHGAP10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl gene 147745303 147745417 . - . gene_id "ENSG00000252951"; gene_version "1"; gene_name "RNA5SP165"; gene_source "ensembl"; gene_biotype "rRNA_pseudogene"; +chr4 mirbase gene 147782595 147782668 . + . gene_id "ENSG00000264274"; gene_version "1"; gene_name "MIR4799"; gene_source "mirbase"; gene_biotype "miRNA"; +chr4 ensembl gene 147808926 147809209 . + . gene_id "ENSG00000240014"; gene_version "3"; gene_name "RN7SL254P"; gene_source "ensembl"; gene_biotype "misc_RNA"; +chr4 havana gene 147916529 147917386 . - . gene_id "ENSG00000270387"; gene_version "1"; gene_name "AC115621.1"; gene_source 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gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 148819351 148819956 . - . gene_id "ENSG00000279016"; gene_version "1"; gene_name "AC093648.1"; gene_source "havana"; gene_biotype "TEC"; +chr4 havana gene 148940941 148942378 . - . gene_id "ENSG00000249317"; gene_version "1"; gene_name "AC002460.1"; gene_source "havana"; gene_biotype "processed_transcript"; +chr4 ensembl gene 148991572 148991633 . - . gene_id "ENSG00000239168"; gene_version "1"; gene_name "RNU7-197P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 havana gene 149027445 149062522 . - . gene_id "ENSG00000249752"; gene_version "1"; gene_name "AC108156.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 149147802 149149780 . - . gene_id "ENSG00000250252"; gene_version "1"; gene_name "LINC02430"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 149154295 149278123 . + . gene_id "ENSG00000248210"; gene_version "1"; gene_name "LINC02355"; gene_source "havana"; 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gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 ensembl_havana gene 152779937 152918463 . + . gene_id "ENSG00000164144"; gene_version "15"; gene_name "ARFIP1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 152796063 152796831 . - . gene_id "ENSG00000250980"; gene_version "1"; gene_name "AC113155.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 152927446 152928207 . + . gene_id "ENSG00000231841"; gene_version "1"; gene_name "FAM192BP"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 152936352 152979696 . + . gene_id "ENSG00000137460"; gene_version "8"; gene_name "FHDC1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 153034211 153091165 . + . gene_id "ENSG00000249022"; gene_version "1"; gene_name "AC093599.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 153152342 153339320 . + . gene_id "ENSG00000109654"; 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155458870 155459563 . - . gene_id "ENSG00000249386"; gene_version "1"; gene_name "MTCO2P9"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 155459704 155461237 . - . gene_id "ENSG00000251223"; gene_version "1"; gene_name "MTCO1P9"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 155461633 155462663 . - . gene_id "ENSG00000248907"; gene_version "1"; gene_name "MTND2P33"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 155462873 155463823 . - . gene_id "ENSG00000251407"; gene_version "1"; gene_name "MTND1P22"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 155515727 155517459 . + . gene_id "ENSG00000251244"; gene_version "1"; gene_name "AC107208.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 155666711 155732349 . + . gene_id "ENSG00000164116"; gene_version "16"; gene_name "GUCY1A1"; gene_source "ensembl_havana"; gene_biotype 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gene_name "TRIML2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 188106558 188106914 . + . gene_id "ENSG00000241011"; gene_version "1"; gene_name "AC108073.2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 188121531 188121634 . - . gene_id "ENSG00000201085"; gene_version "1"; gene_name "RNU6-173P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 ensembl_havana gene 188139419 188147743 . + . gene_id "ENSG00000184108"; gene_version "7"; gene_name "TRIML1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 188140822 188143379 . - . gene_id "ENSG00000247130"; gene_version "2"; gene_name "AC138781.1"; gene_source "havana"; gene_biotype "antisense"; +chr4 havana gene 188160065 188161139 . + . gene_id "ENSG00000248370"; gene_version "1"; gene_name "LINC02434"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 188349376 188350024 . - . gene_id "ENSG00000242169"; gene_version "2"; gene_name "AC093789.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 188387471 188389666 . - . gene_id "ENSG00000248880"; gene_version "1"; gene_name "ICE2P1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 188400736 188681051 . + . gene_id "ENSG00000249378"; gene_version "5"; gene_name "LINC01060"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 188630924 188631747 . + . gene_id "ENSG00000250523"; gene_version "1"; gene_name "AC093909.3"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 188713644 188715442 . + . gene_id "ENSG00000275826"; gene_version "1"; gene_name "AC093909.5"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl gene 188716665 188716725 . - . gene_id "ENSG00000252275"; gene_version "1"; gene_name "RNU7-192P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 havana gene 188738373 188739494 . + . gene_id "ENSG00000180015"; gene_version "12"; gene_name "AC093909.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 188740507 188741281 . - . gene_id "ENSG00000278974"; gene_version "1"; gene_name "AC093909.6"; gene_source "havana"; gene_biotype "TEC"; +chr4 havana gene 188757679 188778979 . + . gene_id "ENSG00000249269"; gene_version "1"; gene_name "AC093909.2"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 188776657 188785511 . + . gene_id "ENSG00000251619"; gene_version "1"; gene_name "LINC02508"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 188777679 188796633 . - . gene_id "ENSG00000250626"; gene_version "2"; gene_name "AC093909.4"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 188990715 189002075 . - . gene_id "ENSG00000250024"; gene_version "1"; gene_name "AC122138.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 189193100 189204877 . + . gene_id "ENSG00000251310"; gene_version "1"; gene_name "AC107391.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 189288677 189291336 . - . gene_id "ENSG00000249877"; gene_version "1"; gene_name "AC105924.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 189472965 189475192 . + . gene_id "ENSG00000205100"; gene_version "2"; gene_name "HSP90AA4P"; gene_source "havana"; gene_biotype "transcribed_processed_pseudogene"; +chr4 havana gene 189659605 189661486 . + . gene_id "ENSG00000250739"; gene_version "1"; gene_name "LINC01262"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 189703881 189704490 . - . gene_id "ENSG00000272566"; gene_version "1"; gene_name "AF250324.1"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl gene 189709539 189709714 . - . gene_id "ENSG00000202215"; gene_version "1"; gene_name "RNU1-51P"; gene_source "ensembl"; gene_biotype "snRNA"; +chr4 havana gene 189780336 189940271 . - . gene_id "ENSG00000245685"; gene_version "6"; gene_name "FRG1-DT"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 189881515 189884868 . + . gene_id "ENSG00000250666"; gene_version "1"; gene_name "LINC01596"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 ensembl_havana gene 189940788 189963204 . + . gene_id "ENSG00000109536"; gene_version "11"; gene_name "FRG1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 189973599 189973847 . - . gene_id "ENSG00000249462"; gene_version "1"; gene_name "MLLT10P2"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 189979902 189982379 . + . gene_id "ENSG00000271307"; gene_version "3"; gene_name "AF146191.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 ensembl_havana gene 189982523 189984871 . - . gene_id "ENSG00000251297"; gene_version "1"; gene_name "TUBB7P"; gene_source "ensembl_havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl gene 190015138 190015255 . + . gene_id "ENSG00000199572"; gene_version "1"; gene_name "RNA5SP174"; gene_source "ensembl"; gene_biotype "rRNA_pseudogene"; +chr4 ensembl gene 190017696 190017814 . + . gene_id "ENSG00000201145"; gene_version "1"; gene_name "RNA5SP175"; gene_source "ensembl"; gene_biotype "rRNA_pseudogene"; +chr4 havana gene 190021407 190022665 . - . gene_id "ENSG00000224807"; gene_version "5"; gene_name "DUX4L9"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 190024351 190027257 . - . gene_id "ENSG00000205097"; gene_version "6"; gene_name "FRG2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 190037916 190038399 . - . gene_id "ENSG00000250053"; gene_version "1"; gene_name "RARRES2P4"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 190041342 190043414 . + . gene_id "ENSG00000214273"; gene_version "4"; gene_name "AGGF1P1"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 190057902 190063005 . - . gene_id "ENSG00000249003"; gene_version "1"; gene_name "CLUHP4"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 havana gene 190064502 190067864 . + . gene_id "ENSG00000281591"; gene_version "1"; gene_name "DBET"; gene_source "havana"; gene_biotype "lincRNA"; +chr4 havana gene 190065233 190065914 . + . gene_id "ENSG00000277162"; gene_version "1"; gene_name "U85056.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 190067935 190069209 . + . gene_id "ENSG00000281720"; gene_version "1"; gene_name "DUX4L8"; gene_source "ensembl_havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 190071232 190072506 . + . gene_id "ENSG00000281652"; gene_version "1"; gene_name "DUX4L7"; gene_source "ensembl_havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 190074525 190075799 . + . gene_id "ENSG00000281058"; gene_version "1"; gene_name "DUX4L6"; gene_source "ensembl_havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 190077818 190079092 . + . gene_id "ENSG00000280799"; gene_version "1"; gene_name "DUX4L5"; gene_source "ensembl_havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 190081118 190082386 . + . gene_id "ENSG00000258834"; gene_version "4"; gene_name "DUX4L4"; gene_source "ensembl_havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 190084412 190085686 . + . gene_id "ENSG00000280757"; gene_version "1"; gene_name "DUX4L1"; gene_source "ensembl_havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 190087705 190088979 . + . gene_id "ENSG00000281627"; gene_version "1"; gene_name "DUX4L3"; gene_source "ensembl_havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 190091005 190092279 . + . gene_id "ENSG00000280457"; gene_version "1"; gene_name "DUX4L2"; gene_source "ensembl_havana"; gene_biotype "unprocessed_pseudogene"; +chr4 ensembl_havana gene 190173774 190185942 . + . gene_id "ENSG00000260596"; gene_version "5"; gene_name "DUX4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +chr4 havana gene 190195727 190196190 . + . gene_id "ENSG00000261914"; gene_version "2"; gene_name "RPL23AP84"; gene_source "havana"; gene_biotype "processed_pseudogene"; +chr4 havana gene 190195738 190195978 . - . gene_id "ENSG00000282994"; gene_version "1"; gene_name "AC215524.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; diff --git a/data/genome_chr4.fa.gz b/data/genome_chr4.fa.gz new file mode 100644 index 0000000..ca00d02 Binary files /dev/null and b/data/genome_chr4.fa.gz differ diff --git a/data/genome_chr4.fa.gz.fai b/data/genome_chr4.fa.gz.fai new file mode 100644 index 0000000..508943a --- /dev/null +++ b/data/genome_chr4.fa.gz.fai @@ -0,0 +1 @@ +chr4 190214555 6 60 61 diff --git a/data/genome_chr4.fa.gz.gzi b/data/genome_chr4.fa.gz.gzi new file mode 100644 index 0000000..58e6a37 Binary files /dev/null and b/data/genome_chr4.fa.gz.gzi differ diff --git a/data/individual_motifs/MA0002.2.jaspar b/data/individual_motifs/MA0002.2.jaspar new file mode 100644 index 0000000..d3c63f4 --- /dev/null +++ b/data/individual_motifs/MA0002.2.jaspar @@ -0,0 +1,5 @@ +>MA0002.2 RUNX1 +A [ 287 234 123 57 0 87 0 17 10 131 500 ] +C [ 496 485 1072 0 75 127 0 42 400 463 158 ] +G [ 696 467 149 7 1872 70 1987 1848 251 81 289 ] +T [ 521 814 656 1936 53 1716 13 93 1339 1325 1053 ] diff --git a/data/individual_motifs/MA0003.3.jaspar b/data/individual_motifs/MA0003.3.jaspar new file mode 100644 index 0000000..35d2a59 --- /dev/null +++ b/data/individual_motifs/MA0003.3.jaspar @@ -0,0 +1,5 @@ +>MA0003.3 TFAP2A +A [ 1706 137 0 0 33 575 3640 1012 0 31 1865 ] +C [ 1939 968 5309 5309 1646 2682 995 224 31 4726 798 ] +G [ 277 4340 139 11 658 1613 618 5309 5309 582 1295 ] +T [ 1386 47 0 281 2972 438 56 0 0 21 1350 ] diff --git a/data/individual_motifs/MA0004.1.jaspar b/data/individual_motifs/MA0004.1.jaspar new file mode 100644 index 0000000..8791d55 --- /dev/null +++ b/data/individual_motifs/MA0004.1.jaspar @@ -0,0 +1,5 @@ +>MA0004.1 Arnt +A [ 4 19 0 0 0 0 ] +C [ 16 0 20 0 0 0 ] +G [ 0 1 0 20 0 20 ] +T [ 0 0 0 0 20 0 ] diff --git a/data/individual_motifs/MA0007.3.jaspar b/data/individual_motifs/MA0007.3.jaspar new file mode 100644 index 0000000..ee373db --- /dev/null +++ b/data/individual_motifs/MA0007.3.jaspar @@ -0,0 +1,5 @@ +>MA0007.3 Ar +A [ 1094 939 8 1197 2167 4 1997 199 561 755 33 0 22 1195 7 32 430 ] +C [ 167 17 0 291 5 2189 20 1228 611 250 277 4 4 112 2166 1542 1092 ] +G [ 1555 2221 3837 184 3 5 273 328 991 1673 8 3618 0 230 0 2 343 ] +T [ 286 19 6 1027 3 2 11 712 509 207 2529 1 2768 1094 8 829 913 ] diff --git a/data/individual_motifs/MA0009.2.jaspar b/data/individual_motifs/MA0009.2.jaspar new file mode 100644 index 0000000..8860eaa --- /dev/null +++ b/data/individual_motifs/MA0009.2.jaspar @@ -0,0 +1,5 @@ +>MA0009.2 T +A [ 52 2241 3816 0 4107 218 2277 629 4161 1066 665 0 12 504 373 4171 ] +C [ 156 4778 55 5262 0 5104 4418 611 121 2004 135 190 0 2352 1237 12 ] +G [ 22 1321 1415 0 141 111 1667 214 491 5819 7304 13 7628 69 7058 111 ] +T [ 6886 254 217 2 0 400 809 6551 417 2921 366 6777 0 5975 1657 17 ] diff --git a/data/individual_motifs/MA0014.3.pfm b/data/individual_motifs/MA0014.3.pfm new file mode 100644 index 0000000..c9265c2 --- /dev/null +++ b/data/individual_motifs/MA0014.3.pfm @@ -0,0 +1,6 @@ +>MA0014.3 PAX5 +540 625 18 18 111 94 16 1243 32 69 377 263 +179 148 151 1276 35 88 37 39 1305 1081 405 403 +578 354 1231 34 1243 30 1355 70 57 118 312 359 +115 285 12 84 23 1200 4 60 18 144 318 387 + diff --git a/data/individual_motifs/MA0017.2.pfm b/data/individual_motifs/MA0017.2.pfm new file mode 100644 index 0000000..432b514 --- /dev/null +++ b/data/individual_motifs/MA0017.2.pfm @@ -0,0 +1,6 @@ +>MA0017.2 NR2F1 +0.204306 0.602538 0.525211 0.691463 0.000000 0.000000 0.000000 0.000000 0.992510 0.424247 0.267767 0.271664 0.116124 +0.486981 0.140310 0.032095 0.000000 0.002482 0.000000 0.000000 1.000000 0.000000 0.253338 0.245957 0.204826 0.059523 +0.139381 0.095613 0.403798 0.308537 0.997518 1.000000 0.000000 0.000000 0.007490 0.134174 0.364458 0.322249 0.753506 +0.169333 0.161539 0.038895 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.188241 0.121818 0.201260 0.070847 + diff --git a/data/individual_motifs/MA0018.3.jaspar b/data/individual_motifs/MA0018.3.jaspar new file mode 100644 index 0000000..2054ee3 --- /dev/null +++ b/data/individual_motifs/MA0018.3.jaspar @@ -0,0 +1,5 @@ +>MA0018.3 CREB1 +A [ 1935 2798 209 127 8337 210 963 150 221 8278 722 2102 ] +C [ 1949 2075 213 223 95 7146 555 292 8303 174 3279 2888 ] +G [ 2888 3279 174 8303 292 555 7146 95 223 213 2075 1949 ] +T [ 2102 722 8278 221 150 963 210 8337 127 209 2798 1935 ] diff --git a/data/individual_motifs/MA0019.1.jaspar b/data/individual_motifs/MA0019.1.jaspar new file mode 100644 index 0000000..d2b30ea --- /dev/null +++ b/data/individual_motifs/MA0019.1.jaspar @@ -0,0 +1,5 @@ +>MA0019.1 Ddit3::Cebpa +A [ 14 11 18 0 0 4 38 36 0 14 4 0 ] +C [ 7 7 3 1 0 33 1 2 6 17 23 26 ] +G [ 12 14 15 0 38 0 0 1 0 5 9 6 ] +T [ 6 7 3 38 1 2 0 0 33 3 3 7 ] diff --git a/data/individual_motifs/MA0024.3.jaspar b/data/individual_motifs/MA0024.3.jaspar new file mode 100644 index 0000000..ffbc71d --- /dev/null +++ b/data/individual_motifs/MA0024.3.jaspar @@ -0,0 +1,5 @@ +>MA0024.3 E2F1 +A [ 254 241 208 54 0 0 0 2 0 524 510 493 ] +C [ 115 46 36 71 32 599 1 588 577 171 80 59 ] +G [ 89 100 145 888 950 0 1009 17 46 20 58 112 ] +T [ 565 638 627 1 0 2 0 0 50 119 182 219 ] diff --git a/data/individual_motifs/MA0025.1.jaspar b/data/individual_motifs/MA0025.1.jaspar new file mode 100644 index 0000000..af4d896 --- /dev/null +++ b/data/individual_motifs/MA0025.1.jaspar @@ -0,0 +1,5 @@ +>MA0025.1 NFIL3 +A [ 1 0 22 0 2 0 23 22 0 7 5 ] +C [ 0 0 0 8 0 0 0 0 11 5 5 ] +G [ 0 2 0 0 21 0 0 1 4 7 3 ] +T [ 22 21 1 15 0 23 0 0 8 4 10 ] diff --git a/data/individual_motifs/MA0027.2.jaspar b/data/individual_motifs/MA0027.2.jaspar new file mode 100644 index 0000000..5c3edaf --- /dev/null +++ b/data/individual_motifs/MA0027.2.jaspar @@ -0,0 +1,5 @@ +>MA0027.2 EN1 +A [ 427 104 2891 2891 0 57 2891 689 ] +C [ 1174 1328 99 28 0 483 0 683 ] +G [ 765 5 71 0 0 162 30 1216 ] +T [ 525 1562 0 0 2891 2891 132 302 ] diff --git a/data/individual_motifs/MA0028.2.pfm b/data/individual_motifs/MA0028.2.pfm new file mode 100644 index 0000000..216aefc --- /dev/null +++ b/data/individual_motifs/MA0028.2.pfm @@ -0,0 +1,6 @@ +>MA0028.2 ELK1 +0.681307 0.024970 0.007763 0.000000 0.000086 0.993063 0.947111 0.058588 0.016914 0.289781 +0.040902 0.939862 0.990507 0.000458 0.000880 0.005051 0.006885 0.045864 0.116499 0.145676 +0.192745 0.030325 0.001276 0.998975 0.983722 0.001344 0.001241 0.889836 0.020737 0.377082 +0.085046 0.004842 0.000454 0.000567 0.015312 0.000542 0.044764 0.005711 0.845850 0.187460 + diff --git a/data/individual_motifs/MA0029.1.jaspar b/data/individual_motifs/MA0029.1.jaspar new file mode 100644 index 0000000..5d59c11 --- /dev/null +++ b/data/individual_motifs/MA0029.1.jaspar @@ -0,0 +1,5 @@ +>MA0029.1 Mecom +A [ 14 20 0 27 1 27 26 0 27 0 24 23 6 15 ] +C [ 2 1 1 0 10 0 0 0 0 3 1 0 7 6 ] +G [ 6 2 25 0 0 0 1 27 0 0 0 4 7 3 ] +T [ 5 4 1 0 16 0 0 0 0 24 2 0 7 3 ] diff --git a/data/individual_motifs/MA0030.1.jaspar b/data/individual_motifs/MA0030.1.jaspar new file mode 100644 index 0000000..2fff565 --- /dev/null +++ b/data/individual_motifs/MA0030.1.jaspar @@ -0,0 +1,5 @@ +>MA0030.1 FOXF2 +A [ 1 10 17 13 3 7 0 27 27 27 0 27 16 7 ] +C [ 10 7 4 5 11 0 0 0 0 0 25 0 4 4 ] +G [ 7 5 2 5 8 20 0 0 0 0 0 0 2 6 ] +T [ 9 5 4 5 0 0 27 0 0 0 2 0 5 10 ] diff --git a/data/individual_motifs/MA0031.1.jaspar b/data/individual_motifs/MA0031.1.jaspar new file mode 100644 index 0000000..e6e0b60 --- /dev/null +++ b/data/individual_motifs/MA0031.1.jaspar @@ -0,0 +1,5 @@ +>MA0031.1 FOXD1 +A [ 1 0 19 20 18 1 20 7 ] +C [ 1 0 1 0 1 18 0 2 ] +G [ 17 0 0 0 1 0 0 3 ] +T [ 1 20 0 0 0 1 0 8 ] diff --git a/data/individual_motifs/MA0032.2.jaspar b/data/individual_motifs/MA0032.2.jaspar new file mode 100644 index 0000000..1517b17 --- /dev/null +++ b/data/individual_motifs/MA0032.2.jaspar @@ -0,0 +1,5 @@ +>MA0032.2 FOXC1 +A [ 6452 14324 7893 4858 2496 13117 18489 18489 122 18489 6702 ] +C [ 772 728 2008 336 1652 5372 108 56 8782 27 1558 ] +G [ 304 4165 2422 13631 390 21 0 141 165 433 1107 ] +T [ 12038 1386 10596 51 18489 45 57 112 9708 184 11787 ] diff --git a/data/individual_motifs/MA0033.2.jaspar b/data/individual_motifs/MA0033.2.jaspar new file mode 100644 index 0000000..7c8295a --- /dev/null +++ b/data/individual_motifs/MA0033.2.jaspar @@ -0,0 +1,5 @@ +>MA0033.2 FOXL1 +A [ 2102 10 4780 4780 4780 0 4780 ] +C [ 13 416 628 38 82 3723 54 ] +G [ 2678 0 57 0 50 0 0 ] +T [ 140 4780 0 15 0 1057 17 ] diff --git a/data/individual_motifs/MA0035.3.jaspar b/data/individual_motifs/MA0035.3.jaspar new file mode 100644 index 0000000..528e793 --- /dev/null +++ b/data/individual_motifs/MA0035.3.jaspar @@ -0,0 +1,5 @@ +>MA0035.3 Gata1 +A [ 2035 506 0 0 0 17955 0 0 2166 2502 1886 ] +C [ 4321 6406 14869 697 0 0 0 17955 0 6166 5072 ] +G [ 2530 2792 437 0 0 0 0 0 0 6687 1598 ] +T [ 9069 8251 2649 17258 17955 0 17955 0 15789 2600 9399 ] diff --git a/data/individual_motifs/MA0036.3.jaspar b/data/individual_motifs/MA0036.3.jaspar new file mode 100644 index 0000000..93e6e38 --- /dev/null +++ b/data/individual_motifs/MA0036.3.jaspar @@ -0,0 +1,5 @@ +>MA0036.3 GATA2 +A [ 3303 1986 940 444 417 14098 145 96 2373 2912 3278 ] +C [ 2978 4099 10607 259 34 14 77 13786 492 3714 3874 ] +G [ 3201 2966 1223 150 21 43 48 126 367 3656 2216 ] +T [ 4731 5162 1443 13360 13741 58 13943 205 10981 3931 4845 ] diff --git a/data/individual_motifs/MA0037.3.jaspar b/data/individual_motifs/MA0037.3.jaspar new file mode 100644 index 0000000..e94df92 --- /dev/null +++ b/data/individual_motifs/MA0037.3.jaspar @@ -0,0 +1,5 @@ +>MA0037.3 GATA3 +A [ 502 0 999 0 914 862 114 423 ] +C [ 226 0 0 0 2 15 301 188 ] +G [ 1 999 0 0 0 76 476 321 ] +T [ 271 0 0 999 83 47 109 68 ] diff --git a/data/individual_motifs/MA0038.1.jaspar b/data/individual_motifs/MA0038.1.jaspar new file mode 100644 index 0000000..4184481 --- /dev/null +++ b/data/individual_motifs/MA0038.1.jaspar @@ -0,0 +1,5 @@ +>MA0038.1 Gfi1 +A [ 9 28 53 53 1 1 31 8 19 7 ] +C [ 20 16 0 0 0 52 7 28 11 13 ] +G [ 9 7 0 0 1 0 2 11 2 28 ] +T [ 15 2 0 0 51 0 13 6 21 5 ] diff --git a/data/individual_motifs/MA0039.3.jaspar b/data/individual_motifs/MA0039.3.jaspar new file mode 100644 index 0000000..6d0605b --- /dev/null +++ b/data/individual_motifs/MA0039.3.jaspar @@ -0,0 +1,5 @@ +>MA0039.3 KLF4 +A [ 262 117 924 8 830 13 29 15 259 184 230 ] +C [ 481 648 14 948 2 914 909 933 72 279 295 ] +G [ 126 105 18 6 123 18 17 4 39 283 202 ] +T [ 100 99 13 7 14 24 14 17 599 223 242 ] diff --git a/data/individual_motifs/MA0040.1.jaspar b/data/individual_motifs/MA0040.1.jaspar new file mode 100644 index 0000000..16f9f9c --- /dev/null +++ b/data/individual_motifs/MA0040.1.jaspar @@ -0,0 +1,5 @@ +>MA0040.1 Foxq1 +A [ 4 13 5 3 0 0 0 0 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mode 100644 index 0000000..904a0e1 --- /dev/null +++ b/data/individual_motifs/MA0830.1.pfm @@ -0,0 +1,6 @@ +>MA0830.1 TCF4 +4738 7822 6 20335 0 56 117 27 374 5305 +8284 2465 20335 0 20335 20335 0 5 7336 4812 +2128 9640 0 0 2315 387 0 20335 6324 4838 +5185 409 13 0 1334 0 20335 25 6301 5380 + diff --git a/data/individual_motifs/MA0834.1.pfm b/data/individual_motifs/MA0834.1.pfm new file mode 100644 index 0000000..a17bee1 --- /dev/null +++ b/data/individual_motifs/MA0834.1.pfm @@ -0,0 +1,6 @@ +>MA0834.1 ATF7 +0.202897 0.265391 0.822161 0.000567 0.001231 0.995981 0.001028 0.004068 0.001286 0.122081 0.996803 0.003020 0.291169 0.293829 +0.341749 0.126229 0.015653 0.000206 0.000331 0.000412 0.993779 0.000463 0.000823 0.874615 0.000103 0.269001 0.419887 0.254513 +0.215261 0.377600 0.160442 0.002218 0.915156 0.002989 0.001697 0.995263 0.003959 0.002308 0.002527 0.016203 0.110145 0.304795 +0.240093 0.230781 0.001744 0.997008 0.083282 0.000618 0.003496 0.000206 0.993932 0.000995 0.000567 0.711776 0.178799 0.146863 + diff --git a/data/individual_motifs/MA1101.1.jaspar b/data/individual_motifs/MA1101.1.jaspar new file mode 100644 index 0000000..ef4a407 --- /dev/null +++ b/data/individual_motifs/MA1101.1.jaspar @@ -0,0 +1,5 @@ +>MA1101.1 BACH2 +A [ 361 852 11 22 1841 73 110 61 1814 45 79 1334 512 530 ] +C [ 492 519 19 14 19 1441 15 1799 13 48 1680 160 404 369 ] +G [ 682 423 10 1787 15 291 30 14 31 1639 86 171 501 294 ] +T [ 360 101 1855 72 20 90 1740 21 37 163 50 230 478 702 ] diff --git a/data/individual_motifs/MA1108.1.pfm b/data/individual_motifs/MA1108.1.pfm new file mode 100644 index 0000000..85f9222 --- /dev/null +++ b/data/individual_motifs/MA1108.1.pfm @@ -0,0 +1,6 @@ +>MA1108.1 MXI1 +0.194167 0.220902 0.374021 0.102079 0.015393 0.953551 0.004321 0.019714 0.005401 0.005401 0.091817 0.181204 0.142857 +0.325952 0.302998 0.223602 0.717796 0.961113 0.012962 0.944910 0.015663 0.029706 0.024305 0.478531 0.312449 0.359168 +0.311369 0.328382 0.260600 0.131245 0.014583 0.026195 0.012152 0.963543 0.008642 0.958682 0.299487 0.279503 0.286524 +0.168512 0.147718 0.141777 0.048879 0.008912 0.007291 0.038617 0.001080 0.956252 0.011612 0.130165 0.226843 0.211450 + diff --git a/data/individual_motifs/MA1114.1.pfm b/data/individual_motifs/MA1114.1.pfm new file mode 100644 index 0000000..4dad0a7 --- /dev/null +++ b/data/individual_motifs/MA1114.1.pfm @@ -0,0 +1,6 @@ +>MA1114.1 PBX3 +0.227176 0.215069 0.188007 0.084888 0.032474 0.915254 0.047714 0.035180 0.020795 0.877938 0.021364 0.867540 0.052557 0.125908 0.178180 0.266201 0.212933 +0.243697 0.245549 0.263353 0.032047 0.032332 0.017804 0.112235 0.028344 0.034468 0.015382 0.929212 0.018373 0.058681 0.196126 0.378009 0.230594 0.256516 +0.312206 0.275459 0.274605 0.071642 0.912406 0.030480 0.702037 0.040593 0.932916 0.086028 0.029768 0.060533 0.810568 0.580687 0.226606 0.294545 0.315767 +0.216921 0.263923 0.274035 0.811423 0.022789 0.036462 0.138015 0.895884 0.011822 0.020652 0.019655 0.053554 0.078194 0.097280 0.217206 0.208660 0.214784 + diff --git a/data/individual_motifs/MA1117.1.pfm b/data/individual_motifs/MA1117.1.pfm new file mode 100644 index 0000000..0e489ce --- /dev/null +++ b/data/individual_motifs/MA1117.1.pfm @@ -0,0 +1,6 @@ +>MA1117.1 RELB +0.241945 0.374164 0.861094 0.063830 0.027356 0.043769 0.027964 0.044377 0.024012 0.241945 0.216109 +0.125836 0.170517 0.038602 0.032523 0.031307 0.889970 0.941641 0.915805 0.922492 0.190881 0.279939 +0.478723 0.241337 0.047720 0.048328 0.016109 0.012158 0.008511 0.017629 0.032523 0.299088 0.302736 +0.153495 0.213982 0.052584 0.855319 0.925228 0.054103 0.021884 0.022188 0.020973 0.268085 0.201216 + diff --git a/data/individual_motifs/MA1124.1.pfm b/data/individual_motifs/MA1124.1.pfm new file mode 100644 index 0000000..4056a0b --- /dev/null +++ b/data/individual_motifs/MA1124.1.pfm @@ -0,0 +1,6 @@ +>MA1124.1 ZNF24 +0.088182 0.773601 0.041109 0.018538 0.013989 0.962796 0.004162 0.007810 0.015191 0.945503 0.043340 0.042267 0.088483 +0.731892 0.077927 0.090199 0.023344 0.949923 0.009398 0.038062 0.014161 0.946962 0.017250 0.088483 0.091315 0.759569 +0.057715 0.084406 0.031711 0.019782 0.005064 0.021498 0.005493 0.007810 0.003991 0.025275 0.034801 0.044842 0.036732 +0.122211 0.064066 0.836981 0.938337 0.031025 0.006308 0.952283 0.970220 0.033857 0.011972 0.833376 0.821576 0.115216 + diff --git a/data/individual_motifs/MA1125.1.pfm b/data/individual_motifs/MA1125.1.pfm new file mode 100644 index 0000000..a01baaa --- /dev/null +++ b/data/individual_motifs/MA1125.1.pfm @@ -0,0 +1,6 @@ +>MA1125.1 ZNF384 +0.310847 0.299543 0.312884 0.431275 0.997404 0.992048 0.988138 0.994053 0.992410 0.999113 0.667762 0.621562 +0.162488 0.230835 0.113561 0.252719 0.000230 0.001150 0.000690 0.000427 0.000854 0.000197 0.095554 0.130220 +0.185654 0.168666 0.153715 0.155128 0.000427 0.000624 0.000854 0.000493 0.000460 0.000000 0.090921 0.095226 +0.341011 0.300956 0.419840 0.160878 0.001939 0.006178 0.010318 0.005027 0.006276 0.000690 0.145763 0.152992 + diff --git a/data/individual_motifs/MA1141.1.pfm b/data/individual_motifs/MA1141.1.pfm new file mode 100644 index 0000000..6b56dea --- /dev/null +++ b/data/individual_motifs/MA1141.1.pfm @@ -0,0 +1,6 @@ +>MA1141.1 FOS::JUND +0.183000 0.181818 0.592408 0.000000 0.000000 0.894000 0.074925 0.000000 0.029029 1.000000 0.021000 0.250000 0.264000 +0.244000 0.166833 0.103896 0.001000 0.000000 0.091000 0.039960 0.000000 0.970971 0.000000 0.290000 0.370000 0.264000 +0.315000 0.388611 0.265734 0.000000 0.871000 0.000000 0.866134 0.000000 0.000000 0.000000 0.077000 0.195000 0.292000 +0.258000 0.262737 0.037962 0.999000 0.129000 0.015000 0.018981 1.000000 0.000000 0.000000 0.612000 0.185000 0.180000 + diff --git a/data/individual_motifs/MA1419.1.pfm b/data/individual_motifs/MA1419.1.pfm new file mode 100644 index 0000000..2a345de --- /dev/null +++ b/data/individual_motifs/MA1419.1.pfm @@ -0,0 +1,6 @@ +>MA1419.1 IRF4 +0.230488 0.007038 0.007646 0.992838 0.989587 0.999603 0.004012 0.000549 0.001256 0.998722 0.977657 0.999295 0.016419 0.029322 0.555943 +0.416413 0.876486 0.001442 0.002716 0.000175 0.000132 0.972601 0.922055 0.000132 0.001013 0.000237 0.000331 0.897804 0.374545 0.102356 +0.046437 0.001682 0.990235 0.001993 0.000546 0.000088 0.012723 0.000081 0.998546 0.000154 0.000496 0.000088 0.084193 0.005387 0.124504 +0.306662 0.114793 0.000677 0.002453 0.009693 0.000176 0.010663 0.077314 0.000066 0.000110 0.021610 0.000287 0.001584 0.590746 0.217198 + diff --git a/environments/macs.yaml b/environments/macs.yaml new file mode 100644 index 0000000..2717441 --- /dev/null +++ b/environments/macs.yaml @@ -0,0 +1,8 @@ +name: MACS_ENV + +channels: + - bioconda + - conda-forge + +dependencies: + - macs2 diff --git a/environments/tobias.yaml b/environments/tobias.yaml new file mode 100644 index 0000000..f82a0ee --- /dev/null +++ b/environments/tobias.yaml @@ -0,0 +1,52 @@ +name: TOBIAS_ENV + +channels: + - bioconda + - conda-forge + +dependencies: + - python >= 3 + - pysam + - pybigwig + - moods + - pybedtools + - cython + - matplotlib + - numpy + - scipy + - pypdf2 + - scikit-learn + - snakemake + - bedtools + - uropa + - igvtools + - openjdk + - xlsxwriter + - cloudpickle = 0.5.6 + - unzip + - r-base + - r-devtools + - r-shiny + - r-data.table + - r-ggplot2 + - r-plotly + - bioconductor-deseq2 + - r-plyr + - r-scales + - r-rjson + - r-shinydashboard + - r-reshape + - r-ggrepel >= 0.6.12 + - r-heatmaply >= 0.14.1 + - r-colorspace + - r-shinyjs + - r-viridis + - r-rje + - r-openssl + - r-shinycssloaders + - r-log4r + - r-shinythemes + - r-shinybs + - pip: + - adjustText + - tobias \ No newline at end of file diff --git a/example_config.yaml b/example_config.yaml new file mode 100644 index 0000000..c116b16 --- /dev/null +++ b/example_config.yaml @@ -0,0 +1,25 @@ +#-------------------------------------------------------------------------# +#-------------------------- TOBIAS input data ----------------------------# +#-------------------------------------------------------------------------# + +data: + Bcell: [data/Bcell_chr4.bam] #list of .bam-files + Tcell: [data/Tcell_chr4_1.bam, data/Tcell_chr4_2.bam] #list of .bam-files + +run_info: + organism: human #mouse/human + fasta: data/genome_chr4.fa.gz #.fasta-file containing organism genome + blacklist: data/blacklist_chr4.bed #.bed-file containing blacklisted regions + gtf: data/genes_chr4.gtf #.gtf-file for annotation of peaks + motifs: data/individual_motifs #directory containing motifs (single files in MEME/JASPAR/PFM format) + output: test_output #output directory + + +#-------------------------------------------------------------------------# +#----------------------- Default module parameters -----------------------# +#-------------------------------------------------------------------------# + +macs: "--nomodel --shift -100 --extsize 200 --broad" +atacorrect: "" +footprinting: "" +bindetect: "--prefix immune" diff --git a/scripts/convert_data.R b/scripts/convert_data.R new file mode 100644 index 0000000..5667372 --- /dev/null +++ b/scripts/convert_data.R @@ -0,0 +1,38 @@ +# use conda? if not add mirror +if (!require(devtools)) install.packages("devtools", repos="http://cloud.r-project.org/") +if (!require(wilson)) devtools::install_github(repo = "loosolab/wilson", host="github.molgen.mpg.de/api/v3", auth_token = NULL) +if (!require(optparse)) install.packages("optparse", repos="http://cloud.r-project.org/"); library(optparse) + +## utilize snakemake parameter +# Combine list with mandatory parameters with optional parameter list. +# As snakemake provides each element in snakemake@params twice (with/ without name), omit unnamed elements. +# args <- c( +# list(input = snakemake@input[[1]], output = snakemake@output[[1]]), +# snakemake@params[which(names(snakemake@params) != "")] +# ) +# do.call(what = wilson::tobias_parser, args = as.list(args)) + +## utilize command line arguments (called by RScript) +option_list <- list( + make_option(opt_str = c("-i", "--input"), default = NULL, help = "Input bed-file.", metavar = "file"), + make_option(opt_str = c("-o", "--output"), default = NULL, help = "Output file.", metavar = "file"), + make_option(opt_str = c("-c", "--config"), default = NULL, help = "Config json file.", metavar = "file"), + make_option(opt_str = c("-n", "--condition_names"), default = NULL, help = "File with one condition name per row. Used only for columns not defined by config.", metavar = "file") +) + +opt_parser <- OptionParser(option_list = option_list) + +opt <- parse_args(opt_parser) + +# show help if called without arguments +if (length(commandArgs(trailingOnly = TRUE)) <= 0) { + print_help(opt_parser) +} else { + # remove last parameter (help param) + params <- opt[-length(opt)] + # read condition names and store in vector + if (is.element("condition_names", names(params))) { + params$condition_names <- scan(file = params$condition_names, what = character()) + } + do.call(what = wilson::tobias_parser, args = params) +} diff --git a/scripts/install_wilson.R b/scripts/install_wilson.R new file mode 100644 index 0000000..b9aea3e --- /dev/null +++ b/scripts/install_wilson.R @@ -0,0 +1,3 @@ + +if (!require(devtools)) install.packages("devtools", repos="http://cran.us.r-project.org") +if (!require(wilson)) devtools::install_github(repo = "loosolab/wilson", host="github.molgen.mpg.de/api/v3", auth_token = NULL) diff --git a/snakefiles/footprinting.snake b/snakefiles/footprinting.snake new file mode 100644 index 0000000..411d31d --- /dev/null +++ b/snakefiles/footprinting.snake @@ -0,0 +1,93 @@ +# vim: syntax=python tabstop=4 expandtab +# coding: utf-8 + +#--------------------------------------------------------------------------------------------------------# +#Format motifs to pfm format +rule format_motifs: + input: + MOTIF_FILES.values() #MOTIF_FILES is a dict + output: + os.path.join(OUTPUTDIR, "motifs", "all_motifs.txt") + priority: 2 + log: + os.path.join(OUTPUTDIR, "logs", "format_motifs.log") + shell: + "TOBIAS FormatMotifs --input {input} --format pfm --task join --output {output} &> {log}" + +#--------------------------------------------------------------------------------------------------------# +#Correct reads for Tn5 sequence bias +rule atacorrect: + input: + bam = os.path.join(OUTPUTDIR, "mapping", "{condition}.bam"), + peaks = os.path.join(OUTPUTDIR, "peak_calling", "all_merged.bed"), + genome = FASTA + output: + os.path.join(OUTPUTDIR, "bias_correction", "{condition}_uncorrected.bw"), + os.path.join(OUTPUTDIR, "bias_correction", "{condition}_bias.bw"), + os.path.join(OUTPUTDIR, "bias_correction", "{condition}_expected.bw"), + os.path.join(OUTPUTDIR, "bias_correction", "{condition}_corrected.bw"), + params: + "--blacklist " + BLACKLIST if BLACKLIST != "" else "", + "--outdir " + os.path.join(OUTPUTDIR, "bias_correction"), + "--prefix " + "{condition}", + config["atacorrect"] + priority: 2 + threads: 99 #unless there are more than 99 cores, this rule will run on max threads + log: + os.path.join(OUTPUTDIR, "logs", "{condition}_atacorrect.log") + message: + "Running ATACorrect for condition {wildcards.condition} ({input.bam})" + shell: + "TOBIAS ATACorrect -b {input.bam} -g {input.genome} -p {input.peaks} --cores {threads} {params} &> {log}" + + +#--------------------------------------------------------------------------------------------------------# +#Calculate footprint scores per condition +rule footprinting: + input: + signal = os.path.join(OUTPUTDIR, "bias_correction", "{condition}_corrected.bw"), + regions = os.path.join(OUTPUTDIR, "peak_calling", "all_merged.bed") + output: + footprints = os.path.join(OUTPUTDIR, "footprinting", "{condition}_footprints.bw"), + params: + config["footprinting"] + priority: 2 + threads: 99 + log: + os.path.join(OUTPUTDIR, "logs", "{condition}_footprinting.log") + message: + "Running footprinting for condition {wildcards.condition} ({input.signal})" + shell: + "TOBIAS FootprintScores --signal {input.signal} --regions {input.regions} --output {output.footprints} --cores {threads} {params} &> {log}" + + +#--------------------------------------------------------------------------------------------------------# +#Estimate bound sites from scored file +rule bindetect: + input: + motifs = os.path.join(OUTPUTDIR, "motifs", "all_motifs.txt"), + footprints = expand(os.path.join(OUTPUTDIR, "footprinting", "{condition}_footprints.bw"), condition=CONDITION_IDS), + genome = FASTA, + peaks = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated.bed"), + peak_header = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated_header.txt") + output: + bedfiles = expand(os.path.join(OUTPUTDIR, "TFBS", "{TF}", "beds", "{TF}_{suffix}.bed"), TF=TF_IDS, suffix=["all"] + expand("{condition}_{state}", condition=CONDITION_IDS, state=["bound", "unbound"])), + overview = expand(os.path.join(OUTPUTDIR, "TFBS", "{TF}", "{TF}_overview.txt"), TF=TF_IDS), + #figures = os.path.join(OUTPUTDIR, "TFBS", "bindetect_figures.pdf"), + #local = [os.path.join(OUTPUTDIR, "TFBS", fil) for fil in ["bindetect_results.txt", "bindetect_results.xlsx"]], + threads: 99 + priority: 2 + log: + os.path.join(OUTPUTDIR, "logs", "bindetect.log") + params: + "--outdir " + os.path.join(OUTPUTDIR, "TFBS"), + "--cond_names " + " ".join(CONDITION_IDS), + config["bindetect"] + message: + "Running BINDetect" + shell: + "TOBIAS BINDetect --motifs {input.motifs} --signals {input.footprints} --genome {input.genome} --peaks {input.peaks} --peak_header {input.peak_header} --cores {threads} {params} &> {log}; " + "mkdir -p " + os.path.join(OUTPUTDIR, "overview") + ";" + "mv " + os.path.join(OUTPUTDIR, "TFBS", "*.txt") + " " + os.path.join(OUTPUTDIR, "overview") + ";" #move files to overview + "mv " + os.path.join(OUTPUTDIR, "TFBS", "*.xlsx") + " " + os.path.join(OUTPUTDIR, "overview") + ";" + "mv " + os.path.join(OUTPUTDIR, "TFBS", "*.pdf") + " " + os.path.join(OUTPUTDIR, "overview") + ";" \ No newline at end of file diff --git a/snakefiles/helper.snake b/snakefiles/helper.snake new file mode 100644 index 0000000..8e658b8 --- /dev/null +++ b/snakefiles/helper.snake @@ -0,0 +1,46 @@ +import string +import re + +def check_format(file): + + found_format = None + + #Read first nlines of file + nlines = 100 + count = 0 + file_content = "" + with open(file) as f: + for line in f: + count += 1 + file_content += line + + if count == nlines: + break + + #Bed file + if re.match("(^.+\s\d+\s\d+.*\n)+", file_content): + found_format = "bed" + #print("{0} is a .bed-file".format(file)) + + #Jaspar file + elif re.match("(>.+\n([^>]+\n){4})+.*", file_content): + found_format = "jaspar" + #print("{0} is a jaspar pfm file".format(file)) + + #Meme file + elif re.match(".*MEME version.*ALPHABET.*MOTIF.*", file_content, flags=re.DOTALL): + found_format = "meme" + #print("{0} is a meme file".format(file)) + + else: + print("Could not recognize format of file {0}".format(file)) + + return(found_format) + + + +def filafy(astring): #Make name into accepted filename + + valid_chars = "-_.%s%s" % (string.ascii_letters, string.digits) + filename = ''.join(char for char in astring if char in valid_chars) + return(filename) diff --git a/snakefiles/preprocessing.snake b/snakefiles/preprocessing.snake new file mode 100644 index 0000000..1d876f7 --- /dev/null +++ b/snakefiles/preprocessing.snake @@ -0,0 +1,128 @@ +# ------------------------------------------------------------------------------------------------------------------ # +# ------------------------------------------------- Bam processing ------------------------------------------------- # +# ------------------------------------------------------------------------------------------------------------------ # + +# Merge sample bam files to condition bam file +# if only one sample per condition, copy sample bam to merged bam file name for further processing +rule conditionbam: + input: + lambda wildcards: config["data"][wildcards.condition] + output: + bam = os.path.join(OUTPUTDIR, "mapping", "{condition}.bam"), + bai = os.path.join(OUTPUTDIR, "mapping", "{condition}.bam.bai") + threads: 2 + message: "Joining individual bamfiles from condition {wildcards.condition}" + run: + if len(input) > 1: + shell("samtools merge -@ {threads} {output.bam} {input}") + shell("samtools index {output.bam}") + else: + shell("cp {input} {output.bam}") + shell("samtools index {output.bam}") + + +# ------------------------------------------------------------------------------------------------------------------ # +# --------------------------------------------------- Peak-calling ------------------------------------------------- # +# ------------------------------------------------------------------------------------------------------------------ # + +# Peak-calling +gsizes = {"human":"hs", + "mouse":"mm", + "zebrafish": 1369631918} #https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html + +rule macs: + input: + lambda wildcards: id2bam[wildcards.condition][wildcards.sample_id] + output: + macs = os.path.join(OUTPUTDIR, "peak_calling", "{condition}", "{sample_id}_peaks.broadPeak"), + raw = os.path.join(OUTPUTDIR, "peak_calling", "{condition}", "{sample_id}_raw.bed") + log: os.path.join(OUTPUTDIR, "logs", "{condition}_{sample_id}_peak_calling.log") + message: "Running macs2 with .bam-file: {input}" + params: + "--name {sample_id}", + "--outdir " + os.path.join(OUTPUTDIR, "peak_calling", "{condition}"), + "--gsize " + str(gsizes[config["run_info"]["organism"]]), + config.get("macs", ""), + shell: + "set +u; source activate MACS_ENV;" + "macs2 callpeak -t {input} {params} &> {log}; " + "cp {output.macs} {output.raw}; " + + +# ------------------------------------------------------------------------------------------------------------------ # +# ------------------------------------------------- Peak-processing ------------------------------------------------ # +# ------------------------------------------------------------------------------------------------------------------ # +# process peaks: +# 1. reduce to genomic location columns and sort +# 2. merge peaks per condition +# 3. remove blacklisted regions and add unique peak ids +rule process_peaks: + input: + peaks = lambda wildcards: [os.path.join(OUTPUTDIR, "peak_calling", wildcards.condition, sample_id + "_raw.bed") for sample_id in id2bam[wildcards.condition].keys()], + blacklisted = BLACKLIST + output: + peaks = os.path.join(OUTPUTDIR, "peak_calling", "{condition}_union.bed"), + message: "Processing peaks from condition {wildcards.condition}" + shell: + "cat {input.peaks} | cut -f1-3 | sort -k1,1 -k2,2n | bedtools merge -d 5 | bedtools subtract -a - -b {input.blacklisted} -A | " + "awk '$1 !~ /[M]/' | " + "awk '{{print $s\"\\t{wildcards.condition}\"}}' > {output.peaks}" #add condition name to each peak + +# Union peaks across all conditions +rule merge_condition_peaks: + input: expand(os.path.join(OUTPUTDIR, "peak_calling", "{condition}_union.bed"), condition=CONDITION_IDS) + output: os.path.join(OUTPUTDIR, "peak_calling", "all_merged.bed") + message: "Merging peaks across conditions" + shell: + "cat {input} | sort -k1,1 -k2,2n | bedtools merge -d 5 -c 4 -o collapse > {output}" + +#Config for uropa annotation +rule uropa_config: + input: + bed = os.path.join(OUTPUTDIR, "peak_calling", "all_merged.bed"), + gtf = GTF + params: + config.get("uropa", "") + output: + config = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated.config") + run: + + import json + config = {"queries":[ + {"feature":"gene", "feature.anchor":"start", "distance":[10000,1000], "filter_attribute":"gene_biotype", "attribute_values":"protein_coding", "name":"protein_coding_promoter"}, + {"feature":"gene", "distance":1, "filter_attribute":"gene_biotype", "attribute_values":"protein_coding", "internals":0.1, "name":"protein_coding_internal"}, + {"feature":"gene", "feature.anchor":"start", "distance":[10000,1000], "name":"any_promoter"}, + {"feature":"gene", "distance":1, "internals":0.1, "name":"any_internal"}, + {"feature":"gene", "distance":[100000, 100000], "name":"distal_enhancer"}, + ], + "show_attributes":["gene_name","gene_id","gene_biotype"], + "priority":"True" + } + + config["gtf"] = input.gtf + config["bed"] = input.bed + + string_config = json.dumps(config, indent=4) + + config_file = open(output[0], "w") + config_file.write(string_config) + config_file.close() + +# Peak annotation +# peaks per condition or across conditions, dependent on run info output +rule uropa: + input: + config = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated.config") + output: + finalhits = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated_finalhits.txt"), + peaks = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated.bed"), + header = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated_header.txt"), + threads: 99 + log: os.path.join(OUTPUTDIR, "logs", "uropa.log") + params: + prefix = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated") + shell: + "uropa --input {input.config} --prefix {params.prefix} --threads {threads} --log {log}; " + "head -n 1 {output.finalhits} > {output.header}; " #header + "tail -n +2 {output.finalhits} > {output.peaks}" #bedlines + \ No newline at end of file diff --git a/snakefiles/visualization.snake b/snakefiles/visualization.snake new file mode 100644 index 0000000..3acf6c6 --- /dev/null +++ b/snakefiles/visualization.snake @@ -0,0 +1,95 @@ +#----------------------------------------------------------------# +#---------------------------- Heatmaps --------------------------# +#----------------------------------------------------------------# +""" +#Heatmaps split in bound/unbound within conditions +rule plot_heatmaps_within: + input: + beds = expand(os.path.join(OUTPUTDIR, "TFBS", "{{TF}}", "beds", "{{TF}}_{{condition}}_{state}.bed"), state=["bound", "unbound"]), + tracks = expand(os.path.join(OUTPUTDIR, "bias_correction", "{{condition}}_{track}.bw"), track=["uncorrected", "bias", "expected", "corrected"]) + output: + heatmap = os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots", "{TF}_{condition}_heatmap.pdf") + message: "Plotting heatmap for TF \"{wildcards.TF}\" within \"{wildcards.condition}\"" + params: + "--TFBS_labels Bound Unbound", + "--signal_labels " + " ".join(["uncorrected", "bias", "expected", "corrected"]), + "--title '{TF} heatmap'", + shell: + "TOBIAS PlotHeatmap --TFBS {input.beds} --signals {input.tracks} --output {output.heatmap} {params} >/dev/null" +""" + +#Heatmaps across conditions +rule plot_heatmaps_across: + input: + beds = [expand(os.path.join(OUTPUTDIR, "TFBS", "{{TF}}", "beds", "{{TF}}_" + condition + "_{state}.bed"), state=["bound", "unbound"]) for condition in CONDITION_IDS], + tracks = expand(os.path.join(OUTPUTDIR, "bias_correction", "{condition}_corrected.bw"), condition=CONDITION_IDS) + output: + heatmap = os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots", "{TF}_heatmap_comparison.pdf") + message: "Plotting heatmap for TF \"{wildcards.TF}\"" + params: + beds = " ".join(["--TFBS {0}".format(" ".join(expand(os.path.join(OUTPUTDIR, "TFBS", "{{TF}}", "beds", "{{TF}}_" + condition + "_{state}.bed"), state=["bound", "unbound"]))) for condition in CONDITION_IDS]), + #bed_labels = lambda wildcards, input: " ".join(["--TFBS_labels {0}".format(" ".join(["{0}_{1}".format(condition, state) for condition in CONDITION_IDS] for state in ["bound", "unbound"]))]), + signal_labels = "--signal_labels " + " ".join(CONDITION_IDS), + title = "--title '{TF} heatmap across conditions' " + shell: + "TOBIAS PlotHeatmap --signals {input.tracks} --output {output.heatmap} {params} --share_colorbar >/dev/null" + + + +#----------------------------------------------------------------# +#--------------------------- Aggregates -------------------------# +#----------------------------------------------------------------# + +#Comparison between bound/unbound sets of individual TFs +rule plot_aggregate_within: + input: + TFBS = [os.path.join(OUTPUTDIR, "TFBS", "{TF}", "beds", "{TF}_all.bed")] + [os.path.join(OUTPUTDIR, "TFBS", "{TF}", "beds", "{TF}_{condition}_" + state + ".bed") for state in ["bound", "unbound"]], + signals = [os.path.join(OUTPUTDIR, "bias_correction", "{condition}_" + state + ".bw") for state in ["uncorrected", "expected", "corrected"]], + output: + os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots", "{TF}_{condition}_aggregate.pdf") + log: + os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots", "logs", "{TF}_{condition}_aggregate.log") + message: "Plotting split between bound/unbound around TFBS for TF \"{wildcards.TF}\" in condition \"{wildcards.condition}\"" + params: + "--title 'Bias correction and split for {TF} in condition {condition}'", + "--share_y sites", + "--plot_boundaries", + shell: + "TOBIAS PlotAggregate --TFBS {input.TFBS} --signals {input.signals} --output {output} {params} > {log} " + + +#Aggregates across conditions for all and for bound subsets +rule plot_aggregate_across: + input: + TFBS_all = os.path.join(OUTPUTDIR, "TFBS", "{TF}", "beds", "{TF}_all.bed"), + TFBS_bound = expand(os.path.join(OUTPUTDIR, "TFBS", "{{TF}}", "beds", "{{TF}}_{condition}_bound.bed"), condition=CONDITION_IDS), + signals = expand(os.path.join(OUTPUTDIR, "bias_correction", "{condition}_corrected.bw"), condition=CONDITION_IDS), + output: + all_compare = os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots", "{TF}_aggregate_comparison_all.pdf"), + bound_compare = os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots", "{TF}_aggregate_comparison_bound.pdf"), + all_log = os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots", "logs", "{TF}_aggregate_comparison_all.log"), + bound_log = os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots", "logs", "{TF}_aggregate_comparison_bound.log") + priority: 2 + params: + "--title {0}".format("{TF}"), + "--plot_boundaries", + "--share_y both", + message: "Plotting comparison of cutsite signals for \"{wildcards.TF}\" between conditions" + shell: + "TOBIAS PlotAggregate --TFBS {input.TFBS_all} --signals {input.signals} --output {output.all_compare} {params} > {output.all_log}; " + "TOBIAS PlotAggregate --TFBS {input.TFBS_bound} --signals {input.signals} --output {output.bound_compare} {params} > {output.bound_log};" + + +#----------------------------------------------------------------# +#-------------------- Join pdfs from all TFs --------------------# +#----------------------------------------------------------------# + +rule join_pdfs: + input: + expand(os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots", "{TF}_{{plotname}}.pdf"), TF=TF_IDS) + output: + os.path.join(OUTPUTDIR, "overview", "all_{plotname}.pdf") + message: "Joining {wildcards.plotname} plots from all TFs" + shell: + "TOBIAS MergePDF --input {input} --output {output} >/dev/null" + \ No newline at end of file diff --git a/snakefiles/wilson.snake b/snakefiles/wilson.snake new file mode 100644 index 0000000..fe87675 --- /dev/null +++ b/snakefiles/wilson.snake @@ -0,0 +1,84 @@ +import os +from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider + +HTTP = HTTPRemoteProvider() + +#Download the wilson app +rule wilson_app: + input: + HTTP.remote("github.molgen.mpg.de/loosolab/wilson-apps/archive/master.zip", keep_local = False) + output: + app = os.path.join(OUTPUTDIR, "wilson", "app.R") + log: + os.path.join(OUTPUTDIR, "logs", "wilson_installation.log") + params: + os.path.join(OUTPUTDIR, "wilson") + shell: + "mkdir -p {params}; " + "unzip {input} -d {params}; " + "cp -a {params}/wilson-apps-master/wilson-basic/. {params}; " + "rm -rf {params}/wilson-apps-master/; " + "rm -rf {params}/data/*;" + "Rscript scripts/install_wilson.R &> {log} " + +#Make file of condition names to use for wilson conversion +rule get_condition_names: + output: + os.path.join(OUTPUTDIR, "wilson", "condition_names.txt") #will be deleted when all .clarion were made + params: + "\"{0}\"".format("\n".join(CONDITION_IDS) + "\n") + shell: + "printf {params} > {output}" + +#Convert TF-specific overviews +rule convert_individual_overview: + input: + overview = os.path.join(OUTPUTDIR, "TFBS", "{TF}", "{TF}_overview.txt"), + condition_names = os.path.join(OUTPUTDIR, "wilson", "condition_names.txt"), + app = os.path.join(OUTPUTDIR, "wilson", "app.R") + output: + os.path.join(OUTPUTDIR, "wilson", "data", "{TF}_overview.clarion") + shell: + "Rscript scripts/convert_data.R --input {input.overview} --output {output} --condition_names {input.condition_names} &> /dev/null " + +#Convert global bindetect-output: +rule convert_global_overview: + input: + overview = expand(os.path.join(OUTPUTDIR, "TFBS", "{TF}", "{TF}_overview.txt"), TF=TF_IDS), + condition_names = os.path.join(OUTPUTDIR, "wilson", "condition_names.txt"), + app = os.path.join(OUTPUTDIR, "wilson", "app.R") + output: + os.path.join(OUTPUTDIR, "wilson", "data", "bindetect_results.clarion") + params: + os.path.join(OUTPUTDIR, "overview", "*_results.txt") + shell: + "Rscript scripts/convert_data.R --input {params} --output {output} --condition_names {input.condition_names} &> /dev/null " + +#Howto file for wilson +rule wilson_howto: + input: + individual_overview = expand(os.path.join(OUTPUTDIR, "wilson", "data", "{TF}_overview.clarion"), TF=TF_IDS), + global_overview = os.path.join(OUTPUTDIR, "wilson", "data", "bindetect_results.clarion"), + app = os.path.join(OUTPUTDIR, "wilson", "app.R") + output: + os.path.join(OUTPUTDIR, "wilson", "HOW_TO_WILSON.txt") + run: + + f = open(output[0], "w") + + howto = """The wilson app (https://github.molgen.mpg.de/loosolab/wilson-apps) can be started by running the app.R within the wilson directory. +To do so, run the following code in R (or RStudio): + +'' +if (!require(shiny)) install.packages("shiny"); library(shiny) +""" + howto += "runApp(\"{0}\")\n''\n".format(os.path.abspath(input.app)) + howto += """ +Now your browser will open and you can start using the app. If this is not the case try opening the link displayed in your console manually. + +Note that unlike normal scripts the app will not terminate on its own so please make sure to close the respective process after you are done. +Furthermore, Windows users should install Rtools (https://cran.r-project.org/bin/windows/Rtools/) to enable plot downloading. +""" + + f.write(howto) + f.close()