#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing28701 reads
ln -s . mm10
echo nomatch_run308.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh nomatch_run308.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC3-wt2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC3-wt2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC4-wt3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC4-wt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC5-SET8ko2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC5-SET8ko2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC6-SET8ko3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh ITRC6-SET8ko3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo IPR23r-MEDC.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IPR23r-MEDC.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo IPR30-MEDB.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IPR30-MEDB.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1