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Commit 8e13d400 authored by Christian Arnold's avatar Christian Arnold
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added example from CLL as orientation how to run it

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example/NEW/input/CLL.consensus.5.bed 0 → 100755
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example/NEW/input/cluster.json 0 → 100755
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{
"__default__" :
{
"queue" : "medium_priority",
"nCPUs" : "16",
"memory" : 20000,
"resources" : "\"select[mem>20000] rusage[mem=20000] span[hosts=1]\"",
"name" : "{rule}.{wildcards}",
"output" : "/scratch/carnold/CLL/TF_act_downsampling0.01/output/Logs_and_Benchmarks/{rule}.{wildcards}.out",
"error" : "/scratch/carnold/CLL/TF_act_downsampling0.01/output/Logs_and_Benchmarks/{rule}.{wildcards}.err"
},
"intersectBAM2":
{
"memory" : 1000,
"resources" : "\"select[mem>1000] rusage[mem=1000] span[hosts=1]\""
}
}
example/NEW/input/config.json 0 → 100755
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{
"par_general":
{
"outdir" : "/scratch/carnold/CLL/TF_act_downsampling0.01/output",
"regionExtension" : 100,
"analysisName" : "CLL",
"comparisonType" : "CLL",
"conditionComparison" : "mutated,unmutated",
"designContrast" : "~ Treatment + Condition",
"limit_nTF_to" : -1
},
"samples":
{
"summaryFile" : "/scratch/carnold/CLL/TF_act_downsampling0.01/input/sampleTable_TF.tsv",
"pairedEnd" : true
},
"additionalInputFiles":
{
"peaks_bed" : "/scratch/carnold/CLL/TF_act_downsampling0.01/input/CLL.consensus.5.bed",
"refGenome_fasta" : "/g/scb2/zaugg/zaugg_shared/annotations/hg19/referenceGenome/Bowtie2/hg19.fa",
"dir_PWMScan" : "/g/scb/zaugg/berest/ATACSeq/Analysis/Ackermann/HOCOMOCO.human/PWMscan"
},
"executables":
{
"volcanoPlot1_script" : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/createVolcanoPlot.R",
"prepareData_script" : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/prepareData.R",
"runTFAnalysis_script" : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/runTFAnalysis.R",
"consensusPeaks_script": "",
"permutations_script" : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/permutations.R",
"summarizePermutations_script" : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/summarizePermutations.R",
"preparePermutations_script" : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/preparePermutations.R"
}
}
example/NEW/input/params.sh 0 → 100755
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# Config file to use
configFile="config.json"
snakefile="/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/Snakefile"
# IGNORED NOW, AUTOMATICALLY SET TO 5 WHEN LOCAL 16 OTHERWISE
nCores=16 # Maximum number of CPUs per rule executed. See the separate cluster specification
# Enable various additional output of Snakemake such as verbose messages and printing shell commands
useVerbose=false
useConda=true
# Use a dry run for testing purposes?
dryRun=false
forceRerunAll=false
# Use --notemp for developing purposes: Ignore temp() declarations. This is useful when running only a part of the workflow,
# since temp() would lead to deletion of probably needed files by other parts of the workflow.
ignoreTemp=true
# Default false
touchOutputFiles=false
# Default: Use all rules: Set to ""
allowedRules=""
# Start from only a specific rule? If yes, name the rule here, which has to correspond to the rule name in the Snakefile
runSpecificRule=""
# Run also all downstream rules when runSpecificRule is specified? If set to false, ONLY the specified rule will be run; otherwise, all downstream rules are also triggered
runAlsoDownstreamRules=true
# Cluster options
submitToCluster=true
clusterConfig="cluster.json"
# Maximum number of simultaenous jobs
maxJobsCluster=400
# Maximum number of times a job should be reexecuted when failing
maxRestartsPerJob=2
runCustomCommand=""
# Only execute the last part: Calling Snakemake
skipSummaryAndDAG=true
# You can usually leave this untouched unless you also suffer from the "bug" that dot has a problem producing PDF files. Then change to "svg" pr "png"
workflowGraphFileType="pdf"
example/NEW/input/runSnakefile.sh 0 → 100755
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#!/bin/bash
########################
# PATHS AND PARAMETERS #
########################
# All parameters and paths are defined here:
. "./params.sh"
########################
# RUN AUTOMATED SCRIPT #
########################
. "/g/scb/zaugg/zaugg_shared/scripts/Christian/src/Snakemake/runSnakemakeWrapper.sh"
example/NEW/input/sampleTable_TF.tsv 0 → 100755
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SampleID bamReads Peaks Treatment Condition Gender Mutation conditionSummary
ATAC_50 /scratch/carnold/CLL/Downsampling/output/ATAC_50.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_50.final.stringent.narrowPeak.filtered.bed batch1 mutated F NA mutated
ATAC_244_1 /scratch/carnold/CLL/Downsampling/output/ATAC_244_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_244_1.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_244_2 /scratch/carnold/CLL/Downsampling/output/ATAC_244_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_244_2.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_552_1 /scratch/carnold/CLL/Downsampling/output/ATAC_552_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_552_1.final.stringent.narrowPeak.filtered.bed batch3 unmutated M NA unmutated
ATAC_552_2 /scratch/carnold/CLL/Downsampling/output/ATAC_552_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_552_2.final.stringent.narrowPeak.filtered.bed batch3 unmutated M NA unmutated
ATAC_653_1 /scratch/carnold/CLL/Downsampling/output/ATAC_653_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_653_1.final.stringent.narrowPeak.filtered.bed batch2 unmutated F NA unmutated
ATAC_653_2 /scratch/carnold/CLL/Downsampling/output/ATAC_653_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_653_2.final.stringent.narrowPeak.filtered.bed batch2 unmutated F NA unmutated
ATAC_680_1 /scratch/carnold/CLL/Downsampling/output/ATAC_680_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_680_1.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_680_2 /scratch/carnold/CLL/Downsampling/output/ATAC_680_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_680_2.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_981_1 /scratch/carnold/CLL/Downsampling/output/ATAC_981_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_981_1.final.stringent.narrowPeak.filtered.bed batch3 mutated M NA mutated
ATAC_981_2 /scratch/carnold/CLL/Downsampling/output/ATAC_981_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_981_2.final.stringent.narrowPeak.filtered.bed batch5 mutated M NA mutated
ATAC_1125_1 /scratch/carnold/CLL/Downsampling/output/ATAC_1125_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_1125_1.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_1125_2 /scratch/carnold/CLL/Downsampling/output/ATAC_1125_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_1125_2.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_1303 /scratch/carnold/CLL/Downsampling/output/ATAC_1303.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_1303.final.stringent.narrowPeak.filtered.bed batch1 mutated M NA mutated
ATAC_1781 /scratch/carnold/CLL/Downsampling/output/ATAC_1781.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_1781.final.stringent.narrowPeak.filtered.bed batch4 mutated F NA mutated
ATAC_2132_1 /scratch/carnold/CLL/Downsampling/output/ATAC_2132_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2132_1.final.stringent.narrowPeak.filtered.bed batch3 unmutated F NA unmutated
ATAC_2132_2 /scratch/carnold/CLL/Downsampling/output/ATAC_2132_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2132_2.final.stringent.narrowPeak.filtered.bed batch3 unmutated F NA unmutated
ATAC_2459_1 /scratch/carnold/CLL/Downsampling/output/ATAC_2459_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2459_1.final.stringent.narrowPeak.filtered.bed batch4 mutated M NA mutated
ATAC_2459_2 /scratch/carnold/CLL/Downsampling/output/ATAC_2459_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2459_2.final.stringent.narrowPeak.filtered.bed batch4 mutated M NA mutated
ATAC_2483 /scratch/carnold/CLL/Downsampling/output/ATAC_2483.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2483.final.stringent.narrowPeak.filtered.bed batch4 unmutated F NA unmutated
ATAC_2613_1 /scratch/carnold/CLL/Downsampling/output/ATAC_2613_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2613_1.final.stringent.narrowPeak.filtered.bed batch3 mutated M NA mutated
ATAC_2613_2 /scratch/carnold/CLL/Downsampling/output/ATAC_2613_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2613_2.final.stringent.narrowPeak.filtered.bed batch3 mutated M NA mutated
ATAC_2886_1 /scratch/carnold/CLL/Downsampling/output/ATAC_2886_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2886_1.final.stringent.narrowPeak.filtered.bed batch4 mutated M NA mutated
ATAC_2886_2 /scratch/carnold/CLL/Downsampling/output/ATAC_2886_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2886_2.final.stringent.narrowPeak.filtered.bed batch4 mutated M NA mutated
ATAC_2938_1 /scratch/carnold/CLL/Downsampling/output/ATAC_2938_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2938_1.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_2938_2 /scratch/carnold/CLL/Downsampling/output/ATAC_2938_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2938_2.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_2938_3 /scratch/carnold/CLL/Downsampling/output/ATAC_2938_3.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2938_3.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_2938_4 /scratch/carnold/CLL/Downsampling/output/ATAC_2938_4.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2938_4.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_2938_5 /scratch/carnold/CLL/Downsampling/output/ATAC_2938_5.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2938_5.final.stringent.narrowPeak.filtered.bed batch6 mutated M NA mutated
ATAC_2977_1 /scratch/carnold/CLL/Downsampling/output/ATAC_2977_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2977_1.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_2977_2 /scratch/carnold/CLL/Downsampling/output/ATAC_2977_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_2977_2.final.stringent.narrowPeak.filtered.bed batch6 mutated M NA mutated
ATAC_3069_1 /scratch/carnold/CLL/Downsampling/output/ATAC_3069_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3069_1.final.stringent.narrowPeak.filtered.bed batch3 unmutated F NA unmutated
ATAC_3069_2 /scratch/carnold/CLL/Downsampling/output/ATAC_3069_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3069_2.final.stringent.narrowPeak.filtered.bed batch1 unmutated F NA unmutated
ATAC_3142 /scratch/carnold/CLL/Downsampling/output/ATAC_3142.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3142.final.stringent.narrowPeak.filtered.bed batch4 unmutated F NA unmutated
ATAC_3156_1 /scratch/carnold/CLL/Downsampling/output/ATAC_3156_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3156_1.final.stringent.narrowPeak.filtered.bed batch2 unmutated F NA unmutated
ATAC_3156_2 /scratch/carnold/CLL/Downsampling/output/ATAC_3156_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3156_2.final.stringent.narrowPeak.filtered.bed batch3 unmutated F NA unmutated
ATAC_3215_1 /scratch/carnold/CLL/Downsampling/output/ATAC_3215_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3215_1.final.stringent.narrowPeak.filtered.bed batch4 mutated M NA mutated
ATAC_3215_2 /scratch/carnold/CLL/Downsampling/output/ATAC_3215_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3215_2.final.stringent.narrowPeak.filtered.bed batch4 mutated M NA mutated
ATAC_3215_3 /scratch/carnold/CLL/Downsampling/output/ATAC_3215_3.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3215_3.final.stringent.narrowPeak.filtered.bed batch4 mutated M NA mutated
ATAC_3215_4 /scratch/carnold/CLL/Downsampling/output/ATAC_3215_4.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3215_4.final.stringent.narrowPeak.filtered.bed batch4 mutated M NA mutated
ATAC_3240 /scratch/carnold/CLL/Downsampling/output/ATAC_3240.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3240.final.stringent.narrowPeak.filtered.bed batch4 unmutated M NA unmutated
ATAC_3263_1 /scratch/carnold/CLL/Downsampling/output/ATAC_3263_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3263_1.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_3263_2 /scratch/carnold/CLL/Downsampling/output/ATAC_3263_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3263_2.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_3386 /scratch/carnold/CLL/Downsampling/output/ATAC_3386.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3386.final.stringent.narrowPeak.filtered.bed batch3 mutated M NA mutated
ATAC_3439_1 /scratch/carnold/CLL/Downsampling/output/ATAC_3439_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3439_1.final.stringent.narrowPeak.filtered.bed batch4 mutated F NA mutated
ATAC_3439_2 /scratch/carnold/CLL/Downsampling/output/ATAC_3439_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3439_2.final.stringent.narrowPeak.filtered.bed batch4 mutated F NA mutated
ATAC_3439_3 /scratch/carnold/CLL/Downsampling/output/ATAC_3439_3.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3439_3.final.stringent.narrowPeak.filtered.bed batch4 mutated F NA mutated
ATAC_3492_1 /scratch/carnold/CLL/Downsampling/output/ATAC_3492_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3492_1.final.stringent.narrowPeak.filtered.bed batch4 unmutated F NA unmutated
ATAC_3492_2 /scratch/carnold/CLL/Downsampling/output/ATAC_3492_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3492_2.final.stringent.narrowPeak.filtered.bed batch6 unmutated F NA unmutated
ATAC_3756 /scratch/carnold/CLL/Downsampling/output/ATAC_3756.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3756.final.stringent.narrowPeak.filtered.bed batch6 unmutated F NA unmutated
ATAC_3811 /scratch/carnold/CLL/Downsampling/output/ATAC_3811.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3811.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_3823_1 /scratch/carnold/CLL/Downsampling/output/ATAC_3823_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3823_1.final.stringent.narrowPeak.filtered.bed batch3 mutated M NA mutated
ATAC_3823_2 /scratch/carnold/CLL/Downsampling/output/ATAC_3823_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3823_2.final.stringent.narrowPeak.filtered.bed batch1 mutated M NA mutated
ATAC_3873 /scratch/carnold/CLL/Downsampling/output/ATAC_3873.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3873.final.stringent.narrowPeak.filtered.bed batch4 unmutated F NA unmutated
ATAC_3943 /scratch/carnold/CLL/Downsampling/output/ATAC_3943.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3943.final.stringent.narrowPeak.filtered.bed batch4 unmutated M NA unmutated
ATAC_3980 /scratch/carnold/CLL/Downsampling/output/ATAC_3980.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_3980.final.stringent.narrowPeak.filtered.bed batch4 unmutated M NA unmutated
ATAC_4034 /scratch/carnold/CLL/Downsampling/output/ATAC_4034.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4034.final.stringent.narrowPeak.filtered.bed batch1 mutated F NA mutated
ATAC_4078_1 /scratch/carnold/CLL/Downsampling/output/ATAC_4078_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4078_1.final.stringent.narrowPeak.filtered.bed batch6 unmutated F NA unmutated
ATAC_4078_2 /scratch/carnold/CLL/Downsampling/output/ATAC_4078_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4078_2.final.stringent.narrowPeak.filtered.bed batch3 unmutated F NA unmutated
ATAC_4080 /scratch/carnold/CLL/Downsampling/output/ATAC_4080.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4080.final.stringent.narrowPeak.filtered.bed batch2 mutated M NA mutated
ATAC_4102_1 /scratch/carnold/CLL/Downsampling/output/ATAC_4102_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4102_1.final.stringent.narrowPeak.filtered.bed batch4 mutated M NA mutated
ATAC_4102_2 /scratch/carnold/CLL/Downsampling/output/ATAC_4102_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4102_2.final.stringent.narrowPeak.filtered.bed batch4 mutated M NA mutated
ATAC_4102_3 /scratch/carnold/CLL/Downsampling/output/ATAC_4102_3.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4102_3.final.stringent.narrowPeak.filtered.bed batch4 mutated M NA mutated
ATAC_4189 /scratch/carnold/CLL/Downsampling/output/ATAC_4189.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4189.final.stringent.narrowPeak.filtered.bed batch1 unmutated M NA unmutated
ATAC_4251_1 /scratch/carnold/CLL/Downsampling/output/ATAC_4251_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4251_1.final.stringent.narrowPeak.filtered.bed batch6 unmutated M NA unmutated
ATAC_4251_2 /scratch/carnold/CLL/Downsampling/output/ATAC_4251_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4251_2.final.stringent.narrowPeak.filtered.bed batch6 unmutated M NA unmutated
ATAC_4333 /scratch/carnold/CLL/Downsampling/output/ATAC_4333.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4333.final.stringent.narrowPeak.filtered.bed batch6 unmutated M NA unmutated
ATAC_4621_1 /scratch/carnold/CLL/Downsampling/output/ATAC_4621_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4621_1.final.stringent.narrowPeak.filtered.bed batch3 mutated M NA mutated
ATAC_4621_2 /scratch/carnold/CLL/Downsampling/output/ATAC_4621_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4621_2.final.stringent.narrowPeak.filtered.bed batch5 mutated M NA mutated
ATAC_4621_3 /scratch/carnold/CLL/Downsampling/output/ATAC_4621_3.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4621_3.final.stringent.narrowPeak.filtered.bed batch3 mutated M NA mutated
ATAC_4668_1 /scratch/carnold/CLL/Downsampling/output/ATAC_4668_1.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4668_1.final.stringent.narrowPeak.filtered.bed batch4 unmutated M NA unmutated
ATAC_4668_2 /scratch/carnold/CLL/Downsampling/output/ATAC_4668_2.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4668_2.final.stringent.narrowPeak.filtered.bed batch6 unmutated M NA unmutated
ATAC_4747 /scratch/carnold/CLL/Downsampling/output/ATAC_4747.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4747.final.stringent.narrowPeak.filtered.bed batch7 mutated F NA mutated
ATAC_4784 /scratch/carnold/CLL/Downsampling/output/ATAC_4784.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4784.final.stringent.narrowPeak.filtered.bed batch6 mutated F NA mutated
ATAC_4963 /scratch/carnold/CLL/Downsampling/output/ATAC_4963.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4963.final.stringent.narrowPeak.filtered.bed batch1 mutated M NA mutated
ATAC_4989 /scratch/carnold/CLL/Downsampling/output/ATAC_4989.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_4989.final.stringent.narrowPeak.filtered.bed batch4 unmutated M NA unmutated
ATAC_5044 /scratch/carnold/CLL/Downsampling/output/ATAC_5044.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_5044.final.stringent.narrowPeak.filtered.bed batch6 mutated M NA mutated
ATAC_5048 /scratch/carnold/CLL/Downsampling/output/ATAC_5048.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_5048.final.stringent.narrowPeak.filtered.bed batch4 mutated F NA mutated
ATAC_5129 /scratch/carnold/CLL/Downsampling/output/ATAC_5129.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_5129.final.stringent.narrowPeak.filtered.bed batch2 unmutated F NA unmutated
ATAC_5147 /scratch/carnold/CLL/Downsampling/output/ATAC_5147.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_5147.final.stringent.narrowPeak.filtered.bed batch7 unmutated M NA unmutated
ATAC_5199 /scratch/carnold/CLL/Downsampling/output/ATAC_5199.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_5199.final.stringent.narrowPeak.filtered.bed batch4 unmutated M NA unmutated
ATAC_5204 /scratch/carnold/CLL/Downsampling/output/ATAC_5204.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_5204.final.stringent.narrowPeak.filtered.bed batch1 unmutated M NA unmutated
ATAC_5229 /scratch/carnold/CLL/Downsampling/output/ATAC_5229.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_5229.final.stringent.narrowPeak.filtered.bed batch4 unmutated M NA unmutated
ATAC_5263 /scratch/carnold/CLL/Downsampling/output/ATAC_5263.final.s.downsample0.01.bam /scratch/carnold/CLL/TF_act/input/peaks/ATAC_5263.final.stringent.narrowPeak.filtered.bed batch2 unmutated M NA unmutated
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