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configfile_mm9
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configfile_mm9
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#====================================
# Configuration file for running the ATAC-seq pipeline
# Contains locations of executables and a few genome specific files
# required to execute the pipeline
#====================================
# Picard tool executable
# used for removing PCR duplicates from the ChIP-seq alignment file
picardexec=/home/sourya/packages/PicardTool/picard_version_2.18.14.jar
# HOMER package executable path
HOMERPath=/home/sourya/packages/HOMER/bin/
# deeptools package - directory
DeepToolsDir=/home/sourya/packages/deepTools/deepTools2.0/bin/
# 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/chrom_mm9.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/mm9/mm9.fa
# files containing reference UCSC annotation (.gtf format) corresponding to the reference Chromosome
# applied as an input to HOMER
RefChrAnnotFile=/mnt/BioAdHoc/Groups/vd-vijay/sourya/genomes/Annotation/mm9/mm9.gtf
# file containing blacklisted regions corresponding to this reference genome hg38
# can be downloaded from the link
# https://github.com/Boyle-Lab/Blacklist/tree/master/lists (v2)
# its OK if this parameter is void, but we recommend to provide if the file is available
# file can be gzipped or normal text format
BlackListFile=/mnt/BioAdHoc/Groups/vd-vijay/sourya/genomes/BlackListed_Regions/mm9-blacklist.bed
# executable of ataqv package (https://github.com/ParkerLab/ataqv)
# download the GitHub release (.tar.gz) file, extract it and provide the ataqv executable path here
ATAQVPath=/home/sourya/packages/ataqv/ataqv-1.0.0/bin/ataqv
# we have to also include the TSS file, but have to specify that the user needs to convert their GTF File (gene annotation file) in the TSS format
# so that first two fields of TSS file includes the chromosome name and the TSS coordinate
TSSFile=/mnt/BioAdHoc/Groups/vd-vijay/sourya/genomes/Annotation/mm9/mm9_TSS.gtf