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system.Test_ProstateC.config
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system.Test_ProstateC.config
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// user@ip where the fastq files are stored
UIP="[email protected]"
// location of fastq file in server
NCI_PATH="/g/data3/yo4/Cancer-Epigenetics-Data/WGBS"
// number of cores is 8
N_CORES="8"
// trim?
TRIM="CEGX"
// min coverage for CpG bigwig file
MIN_COV="1"
// output the results
OUTPUT="/home/phuluu/data/WGBS10X_new"
// path to human genome hg19
// GENOME="/share/ClusterShare/biodata/contrib/phuluu/bwa_meth/annotations/hg19/hg19.fa"
GENOME="/home/phuluu/Projects/WGBS10X_new/annotations/hg19/hg19.fa"
// CpG="/home/phuluu/Projects/WGBS10X_new/V02/annotations/hg19/hg19.CpG.bed"
// CHG="/home/phuluu/Projects/WGBS10X_new/V02/annotations/hg19/hg19.CHG.bed"
// CHA="/home/phuluu/Projects/WGBS10X_new/V02/annotations/hg19/hg19.CHA.bed"
// CHC="/home/phuluu/Projects/WGBS10X_new/V02/annotations/hg19/hg19.CHC.bed"
// CHT="/home/phuluu/Projects/WGBS10X_new/V02/annotations/hg19/hg19.CHT.bed"
// GSIZE="/home/phuluu/Projects/WGBS10X_new/V02/annotations/hg19/hg19.chrom.sizes.short"
// CpGislands="/home/phuluu/Projects/WGBS10X_new/V02/annotations/hg19/hg19.CpGislands.bed"
// CpGshores="/home/phuluu/Projects/WGBS10X_new/V02/annotations/hg19/hg19.CpGshores.bed"
// others="/home/phuluu/Projects/WGBS10X_new/V02/annotations/hg19/hg19.others.bed"