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configfile
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#====================================
# Configuration file for running the ChIP-seq pipeline
# Contains locations of executables and a few genome specific files
# required to execute the pipeline
#====================================
# executable of SPP (from the package phantompeakqualtools)
# by Anshul Kundaje et al.
sppexec=/home/sourya/packages/phantompeakqualtools/run_spp.R
# Picard tool executable
# used for removing PCR duplicates from the ChIP-seq alignment file
picardexec=/share/apps/picard-tools/picard-tools-2.7.1/picard.jar
# HOMER package executable path
HOMERPath=/home/sourya/packages/HOMER/bin/
# deeptools package - directory
DeepToolsDir=/home/sourya/packages/deepTools/deepTools2.0/bin/
# R package installed - executable
RPackageExec=/home/sourya/R-3.4.3/bin/Rscript
# file (SQL) required to convert the narrowPeak file to the bigBed format
# check the UCSC web site to download these files
NarrowPeakASFile=/mnt/BioAdHoc/Groups/vd-vijay/sourya/genomes/chrsize/narrowPeak.as
# file (SQL) required to convert the bignarrowPeak file to the bigBed format
# check the UCSC web site to download these files
BigNarrowPeakASFile=/mnt/BioAdHoc/Groups/vd-vijay/sourya/genomes/chrsize/bigNarrowPeak.as
# file (SQL) required to convert the broadPeak file to the bigBed format
# check the UCSC web site to download these files
BroadPeakASFile=/mnt/BioAdHoc/Groups/vd-vijay/sourya/genomes/chrsize/broadPeak.as
# files containing chromosome size information
# two column file storing the size of individual chromosomes
# example: for reference genome hg19, chrom_hg19.sizes
# example: for reference genome hg38, hg38.chrom.sizes
# example: for reference genome mm9, chrom_mm9.sizes
# example: for reference genome mm10, mm10.chrom.sizes
RefChrSizeFile=/mnt/BioAdHoc/Groups/vd-vijay/sourya/genomes/chrsize/hg38.chrom.sizes
# files containing reference chromosome fasta sequence
# example: hg19.fa, mm9.fa, hg38.fa and mm10.fa
RefChrFastaFile=/mnt/BioAdHoc/Groups/vd-vijay/sourya/genomes/Complete_Genome/hg38/hg38.fa
# files containing reference UCSC annotation (.gtf format) corresponding to the reference Chromosome
# applied as an input to HOMER
# example: hg19_UCSC_annotation.gtf, hg38_UCSC_Annotation.gtf, mm9_UCSC_annotation.gtf, mm10_UCSC_Annotation.gtf
RefChrAnnotFile=/mnt/BioAdHoc/Groups/vd-vijay/sourya/genomes/Annotation/hg38/UCSC/hg38_UCSC_Annotation.gtf