From 8e13d4003420fb631c5c01357a2cc156dd3ded57 Mon Sep 17 00:00:00 2001
From: Christian Arnold <christian.arnold@embl.de>
Date: Wed, 14 Jun 2017 14:21:21 +0200
Subject: [PATCH] added example from CLL as orientation how to run it
---
example/NEW/input/CLL.consensus.5.bed | 53122 ++++++++++++++++++++++++
example/NEW/input/cluster.json | 20 +
example/NEW/input/config.json | 43 +
example/NEW/input/params.sh | 52 +
example/NEW/input/runSnakefile.sh | 14 +
example/NEW/input/sampleTable_TF.tsv | 85 +
6 files changed, 53336 insertions(+)
create mode 100755 example/NEW/input/CLL.consensus.5.bed
create mode 100755 example/NEW/input/cluster.json
create mode 100755 example/NEW/input/config.json
create mode 100755 example/NEW/input/params.sh
create mode 100755 example/NEW/input/runSnakefile.sh
create mode 100755 example/NEW/input/sampleTable_TF.tsv
diff --git a/example/NEW/input/CLL.consensus.5.bed b/example/NEW/input/CLL.consensus.5.bed
new file mode 100755
index 0000000..22abf0c
--- /dev/null
+++ b/example/NEW/input/CLL.consensus.5.bed
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diff --git a/example/NEW/input/cluster.json b/example/NEW/input/cluster.json
new file mode 100755
index 0000000..af8f66d
--- /dev/null
+++ b/example/NEW/input/cluster.json
@@ -0,0 +1,20 @@
+{
+ "__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]\""
+ }
+
+
+}
diff --git a/example/NEW/input/config.json b/example/NEW/input/config.json
new file mode 100755
index 0000000..8a80add
--- /dev/null
+++ b/example/NEW/input/config.json
@@ -0,0 +1,43 @@
+{
+
+ "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"
+ }
+
+
+
+
+
+}
diff --git a/example/NEW/input/params.sh b/example/NEW/input/params.sh
new file mode 100755
index 0000000..11a6b2f
--- /dev/null
+++ b/example/NEW/input/params.sh
@@ -0,0 +1,52 @@
+
+# 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"
diff --git a/example/NEW/input/runSnakefile.sh b/example/NEW/input/runSnakefile.sh
new file mode 100755
index 0000000..db06edc
--- /dev/null
+++ b/example/NEW/input/runSnakefile.sh
@@ -0,0 +1,14 @@
+#!/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"
diff --git a/example/NEW/input/sampleTable_TF.tsv b/example/NEW/input/sampleTable_TF.tsv
new file mode 100755
index 0000000..30417dd
--- /dev/null
+++ b/example/NEW/input/sampleTable_TF.tsv
@@ -0,0 +1,85 @@
+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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