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@@ -0,0 +1,206 @@
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README.md

@@ -1,48 +1,50 @@
 # masterJLU2018
 
-De novo motif discovery and evaluation based on footprints identified by TOBIAS
+De novo motif discovery and evaluation based on footprints identified by TOBIAS.
 
-For further information read the [documentation](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki)
+For further information read the [documentation](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki).
 
 ## Dependencies
 * [conda](https://conda.io/docs/user-guide/install/linux.html)
 * [Nextflow](https://www.nextflow.io/)
 * [MEME-Suite](http://meme-suite.org/doc/install.html?man_type=web)
 
 ## Installation
-Start with installing all dependencies listed above. It is required to set the [enviroment paths for meme-suite](http://meme-suite.org/doc/install.html?man_type=web#installingtar).
+1. Start with installing all dependencies listed above (Nextflow, conda, MEME-Suite) and downloading all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018).
+2. It is required to set the [environment paths for meme-suite](http://meme-suite.org/doc/install.html?man_type=web#installingtar).
 this can be done with following commands:
 ```
 export PATH=[meme-suite instalation path]/libexec/meme-[meme-suite version]:$PATH
 export PATH=[meme-suite instalation path]/bin:$PATH
 ```
 
-
-Download all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018).
-The Nextflow-script needs a conda enviroment to run. Nextflow can create the needed enviroment from the given yaml-file.
-On some systems Nextflow exits the run with following error:
-```
-Caused by:
-  Failed to create Conda environment
-  command: conda env create --prefix  --file env.yml
-  status : 143
-  message:
-```
-If this error occurs you have to create the enviroment before starting the pipeline.
-To create this enviroment you need the yml-file from the repository.
-Run the following commands to create the enviroment:
-```console
-path=[Path to given masterenv.yml file]
-conda env create --name masterenv -f=$path
+3. Every other dependency will be automatically installed using conda. For that a conda environment has to be created from the yaml-file given in this repository.
+It is required to create and activate the environment from the yaml-file beforehand.
+This can be done with following commands:
+```condsole
+conda env create -f masterenv.yml
+conda activate masterenv
 ```
-When the enviroment is created, set the variable 'path_env' in the configuration file as the path to it.
 
-**Important Note:** For conda the channel bioconda needs to be set as highest priority! This is required due to two differnt packages with the same name in different channels. For the pipeline the package jellyfish from the channel bioconda is needed and **NOT** the jellyfisch package from the channel conda-forge!
+4. Set the wd parameter in the nextflow.config file as path where the repository is saved. For example: '~/masterJLU2018/'.
+
+
+**Important Note:** For conda the channel bioconda needs to be set as highest priority! This is required due to two different packages with the same name in different channels. For the pipeline the package jellyfish from the channel bioconda is needed and **NOT** the jellyfish package from the channel conda-forge!
+
+
 
 ## Quick Start
 ```console
-nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file]
+nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --organism [mm10|mm9|hg19|hg38]
+```
+
+### Demo run
+There are files provided inside  ./demo/ for a demo run.
+Go to the main directory and run following command:
+```
+nextflow run pipeline.nf --bigwig ./demo/buenrostro50k_chr1_fp.bw --bed ./demo/buenrostro50k_chr1_peaks.bed --genome_fasta ./demo/hg38/hg38_chr1.fa --motif_db ./demo/motif_database/jaspar_vertebrates.meme --out ./demo/buenrostro50k_chr1_out/ --create_known_tfbs_path ./demo/known_tfbs_hg38_chr1/ --organism hg38
 ```
+
 ## Parameters
 For a detailed overview for all parameters follow this [link](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki/Configuration).
 ```
@@ -52,31 +54,34 @@ Required arguments:
 	--genome_fasta		 Path to genome in FASTA-format
 	--motif_db		 Path to motif-database in MEME-format
 	--config		 Path to UROPA configuration file
-	--create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored.
-				 Path can be set as tfbs_path in next run. (Default: './')
-	--out			 Output Directory (Default: './out/')	
-
+ 	--organism 		 Input organism [hg38 | hg19 | mm9 | mm10]
+	--out			 Output Directory (Default: './out/')
+
 Optional arguments:
-	
+
 	--help [0|1]		1 to show this help message. (Default: 0)
 	--tfbs_path 		Path to directory with output from tfbsscan. If given tfbsscan will not be run.
+	--create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored.
+				 Path can be set as tfbs_path in next run. (Default: './')
+	--gtf_path			Path to gtf-file. If path is set the process which creats a gtf-file is skipped.
 
 	Footprint extraction:
 	--window_length INT	This parameter sets the length of a sliding window. (Default: 200)
 	--step INT		This parameter sets the number of positions to slide the window forward. (Default: 100)
 	--percentage INT	Threshold in percent (Default: 0)
+	--max_bp_between INT	If footprints are less than X bases appart the footprints will be merged (Default: 6)
 
-	Filter unknown motifs:
+	Filter motifs:
 	--min_size_fp INT	Minimum sequence length threshold. Smaller sequences are discarded. (Default: 10)
-	--max_size_fp INT	Maximum sequence length threshold. Discards all sequences longer than this value. (Default: 100)
+	--max_size_fp INT	Maximum sequence length threshold. Discards all sequences longer than this value. (Default: 200)
+	--tfbsscan_method [moods|fimo] Method used by tfbsscan. (Default: moods)
 
-	Clustering:
+	Cluster:
 	Sequence preparation/ reduction:
-	--kmer INT		Kmer length (Default: 10)
+	--kmer INT		K-mer length (Default: 10)
 	--aprox_motif_len INT	Motif length (Default: 10)
 	--motif_occurence FLOAT	Percentage of motifs over all sequences. Use 1 (Default) to assume every sequence contains a motif.
 	--min_seq_length Interations	Remove all sequences below this value. (Default: 10)
-
 	Clustering:
 	--global INT		Global (=1) or local (=0) alignment. (Default: 0)
 	--identity FLOAT	Identity threshold. (Default: 0.8)
@@ -88,23 +93,29 @@ Optional arguments:
 	Motif estimation:
 	--min_seq INT 		Sets the minimum number of sequences required for the FASTA-files given to GLAM2. (Default: 100)
 	--motif_min_key INT	Minimum number of key positions (aligned columns) in the alignment done by GLAM2. (Default: 8)
-	--motif_max_key INT	Maximum number of key positions (aligned columns) in the alignment done by GLAM2.f (Default: 20)
-	--iteration INT		Number of iterations done by glam2. More Iterations: better results, higher runtime. (Default: 10000)
-	--tomtom_treshold float	Threshold for similarity score. (Default: 0.01)
+	--motif_max_key INT	Maximum number of key positions (aligned columns) in the alignment done by GLAM2. (Default: 20)
+	--iteration INT		Number of iterations done by GLAM2. More Iterations: better results, higher runtime. (Default: 10000)
+	--tomtom_treshold FLOAT	Threshold for similarity score. (Default: 0.01)
 	--best_motif INT	Get the best X motifs per cluster. (Default: 3)
-
 	Moitf clustering:
-	--cluster_motif	Boolean	If 1 pipeline clusters motifs. If its 0 it does not. (Defaul: 0)
+	--cluster_motif	Boolean	If 1 pipeline clusters motifs. If its 0 it does not. (Default: 0)
 	--edge_weight INT	Minimum weight of edges in motif-cluster-graph (Default: 5)
 	--motif_similarity_thresh FLOAT	Threshold for motif similarity score (Default: 0.00001)
 
 	Creating GTF:
-	--organism [hg38 | hg19 | mm9 | mm10]	Input organism
 	--tissues List/String 	List of one or more keywords for tissue-/category-activity, categories must be specified as in JSON
 				config
 All arguments can be set in the configuration files
  ```
 
+For further information read the [documentation](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki).
 
+## Known issues
 
-For further information read the [documentation](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki)
+For unknown reasons, the tool [MOODS](https://www.cs.helsinki.fi/group/pssmfind/), which is called by the tfbsscan, rarely returns empty bedfiles, the problem is probably with the function _pfm_to_log_odds_. If MOODS does not work as expected and has problems with this function, you will see following error message:
+```
+ERROR
+All motiffiles have less than 2 lines!
+Fix motiffiles and try again.
+```
+There is no known fix so far. As a workaround either restart the pipeline in some hours with the same parameters or change the parameter tfbsscan_method to _fimo_ which forces the tfbsscan to use [fimo](http://meme-suite.org/doc/fimo.html). This methods takes longer but will cause no known error with empty bed files.