#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3714383 reads
ln -s . hg19
echo IT3R59-24-Prol.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh IT3R59-24-Prol.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.314906
echo IT3R60-25-D4plus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh IT3R60-25-D4plus.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.65002
echo IT3R61-26-D8minus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh IT3R61-26-D8minus.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.800413
echo IT3R62-27-D8plus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh IT3R62-27-D8plus.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.766053
echo IT3R63-28-Prol.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh IT3R63-28-Prol.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.640738
echo IT3R64-29-D2plus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh IT3R64-29-D2plus.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.785453
echo IT3R65-30-D4plus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh IT3R65-30-D4plus.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.765628
echo IT3R66-31-D8minus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh IT3R66-31-D8minus.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo IT3R67-32-D8plus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh IT3R67-32-D8plus.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.629193