#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2955844 reads
ln -s . hg19
echo KP3R1_Ctrl1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh KP3R1_Ctrl1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.535659
echo KP3R2_Ctrl2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh KP3R2_Ctrl2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.781092
echo KP3R3_Ctrl3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh KP3R3_Ctrl3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.64473
echo KP3R4_WM1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh KP3R4_WM1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.53146
echo KP3R5_WM2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh KP3R5_WM2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.662651
echo KP3R6_WM3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh KP3R6_WM3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1