#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2155254 reads
ln -s . mm10
echo ITRC17-wt1Br.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC17-wt1Br.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-ko2Br.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC20-ko2Br.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo ITRC21-wt1Eu.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC21-wt1Eu.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo ITRC22-wt2Eu.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC22-wt2Eu.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo ITRC23-ko1Eu.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC23-ko1Eu.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1