#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing25538555 reads
ln -s . mm10
echo ITR51r-Set9ko1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITR51r-Set9ko1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.516068
echo ITR52-Set9ko2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITR52-Set9ko2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.876409
echo ITR53-Set9ko3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITR53-Set9ko3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo ITR54-Set9ko4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITR54-Set9ko4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.865704
echo ITR55-Set9ko5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITR55-Set9ko5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.882917
echo ITR56-Set9ko6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITR56-Set9ko6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.834771
echo ITR57-Set9ko7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITR57-Set9ko7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.850941