#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing4335051 reads
echo IT3R9-wt2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R9-wt2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.701589
echo IT3R10-wt3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R10-wt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.477013
echo IT3R11-wt4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R11-wt4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.858074
echo IT3R12-wt5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R12-wt5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.71956
echo IT3R13-SET9ko3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R13-SET9ko3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.622075
echo IT3R14-SET9ko4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R14-SET9ko4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.847199
echo IT3R15-SET9ko5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R15-SET9ko5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo IT3R16-SET9ko7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R16-SET9ko7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.482582