#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing12384958 reads
ln -s . mm10
echo ITRC11b-wt2EUstrep.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC11b-wt2EUstrep.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo ITRC15-SET8ko1EUstrep.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC15-SET8ko1EUstrep.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo ITRC18-wt2Br.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC18-wt2Br.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo ITRC20-SET8ko2Br.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC20-SET8ko2Br.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1