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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"
}
}