#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3670897 reads
echo IT3R23-wt6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R23-wt6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.540582
echo IT3R24-wt7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R24-wt7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.86095
echo IT3R25-wt8.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R25-wt8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.516023
echo IT3R26-wt9.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R26-wt9.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.665028
echo IT3R27-ko4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R27-ko4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.65136
echo IT3R28-ko5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R28-ko5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.60219
echo IT3R29-ko6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R29-ko6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.917403
echo IT3R30-ko7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R30-ko7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.78318
echo IT3R31-wt4TCP36.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R31-wt4TCP36.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.794703
echo IT3R32-wt5TCP36.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R32-wt5TCP36.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.584977
echo IT3R33-ko4TCP36.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R33-ko4TCP36.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo IT3R34-ko5TCP36.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R34-ko5TCP36.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.633371