configfile

#==================================== 
# 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/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