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pHDee/umbrella-config-file.txt
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| # -------------------------------- | |
| # One config file to rule them all | |
| # -------------------------------- | |
| # Author: Sarvesh Nikumbh | |
| # Email: snikumbh@mpi-inf.mpg.de | |
| # Date: May 07, 2018 | |
| # License: | |
| # | |
| # ------------------------------------------------------ | |
| # A. Experiments: Specify the all the samples to process | |
| # ------------------------------------------------------ | |
| pHDee.inner_sample_names = s1 | |
| pHDee.outer_sample_names = CTCF | |
| # ^ CTCF SMC1 H3K4me2 H3K4me3 H3K27ac_A H3K27ac_D | |
| pHDee.replicate = repl1 | |
| # ^ Possible replicate names : repl1/repl2/'' (<blank>) | |
| pHDee.condition = untreated | |
| # ^ Possible values for condition: untreated/dox/tumor | |
| pHDee.experiment_type = HiChIP | |
| pHDee.celltype = A673sh | |
| pHDee.bam_or_fastq = fastq | |
| pHDee.input_folder = test_folder/input_folder | |
| pHDee.output_folder = test_folder/output_folder | |
| pHDee.resolutions = 1000000 | |
| # ^ Expects a list of values (at least 1), e.g., | |
| # 1000000 500000 250000 150000 100000 50000 25000 | |
| pHDee.err_log = pHDee_err.log | |
| # ---------------------------------------------- | |
| # B. Run HiC-Pro using the following config file | |
| # ---------------------------------------------- | |
| pHDee.hicpro.path = /home/snikumbh/working_folder/bin/HiC-Pro_2.9.0 | |
| pHDee.hicpro.config_filename = config-hicpro.txt | |
| pHDee.hicpro.input_folder_suffix = _HiC-Pro_input | |
| pHDee.hicpro.output_folder_suffix = _HiC-Pro_output | |
| pHDee.hicpro.allValidPairs_suffix = _allValidPairs | |
| pHDee.hicpro.output_file = hicpro_cmd.out | |
| # ----------------------------- | |
| # C. Run Fit-Hi-C (requires: C) | |
| # ----------------------------- | |
| pHDee.fithic.output_folder = Fit-Hi-C | |
| pHDee.fithic.noOfBins = 200 | |
| pHDee.fithic.distUpThres = 250000 | |
| pHDee.fithic.distLowThres = 1000 | |
| pHDee.fithic.output_log = run_fithic.out | |
| # ------------------ | |
| # D. Run HiCPlotter | |
| # ------------------ | |
| pHDee.hicplotter.output_folder = hicplotter_results | |
| # ^ This folder is placed under the hicpro_output_folder | |
| pHDee.hicplotter.whole_genome = True | |
| # ^ Possible values: True/False | |
| pHDee.hicplotter.per_chromosome = False | |
| # ^ Possible values: True/False | |
| pHDee.hicplotter.given_chromosome = | |
| # ^ If whole_genome is True, given_chromosome is ignored -- hence can be left blank or not | |
| # ^ If per_chromosome is True, given_chromosome is ignored -- hence can be left blank or not | |
| # ^ If you wish to plot matrix for just one chromosome, set per_chromosome and whole_genome, both, to False, and set given_chromosome | |
| # ^ Prefix the chromosome with 'chr', i.e. use chr19 for chromosome 19 | |
| # ----------------------------------- | |
| # E. Other/Miscellaneous capabilities | |
| # ----------------------------------- | |
| pHDee.suggest_appropriate_resolution = True | |
| # ^ Not used yet; under #TODO | |
| # --------------------------------------------------------------------------------- | |
| # F. Perform hicpro2juicebox conversion (requires: allValidPairs file from HiC-Pro) | |
| # --------------------------------------------------------------------------------- | |
| pHDee.juicebox.output_folder = /home/snikumbh/SL4_working_folder/HiChIP/converted_hic_files_for_juicebox | |
| pHDee.juicebox.independent_folder = True | |
| # ^ Setting independent_folder True, tells the pipeline that the juicebox output_folder is to be treated as an absolute path | |
| # otherwise, the output_folder is treated as relative, and is under hicpro_output_folder | |
| # ^ Although this may not be needed mostly, but this provision avoids disk-space issues | |
| pHDee.juicebox.temp_folder = tmp | |
| # ^ **IMPORTANT**: Ensure that no two pipeline runs (juicebox stages) use the same temp_folder | |
| pHDee.juicebox.jar_file = /home/snikumbh/SL2_working_folder/softwares-install/juicer_tools.1.8.9_jcuda.0.8.jar | |
| pHDee.juicebox.hicpro2juicebox_script = scripts/hicpro2juicebox.sh | |
| pHDee.juicebox.script_output_file = hicpro2juicebox_script.out | |
| pHDee.juicebox.genome_size_file = hg19.chrom.sizes | |
| # --------------------------------- | |
| # H. Call differential interactions | |
| # --------------------------------- | |
| pHDee.hiccompare.output_folder = hiccompare_results | |
| # ^ This folder is placed under the hicpro_output_folder | |
| pHDee.hiccompare.resolutions = 1000000 500000 | |
| # ^ For same set of values as pHDee.resolutions above, copy paste the same list here | |
| pHDee.hiccompare.matrix_type = raw | |
| pHDee.hiccompare.groups_info_file = scripts/make_differential_comparisons/groups.info | |
| pHDee.hiccompare.group_id = 10 | |
| # ^ a list of group ids from among those in the file | |
| pHDee.hiccompare.dist_norm_plots_folder = Distance-normalization-plots | |
| pHDee.hiccompare.md_plots_folder = MD-plots | |
| pHDee.hiccompare.csv_folder = CSV | |
| # ^ The above three folders are placed under the group folder (with name <group_id>) |