#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing15196514 reads
ln -s . mm10
echo ITC274-PolII-wt3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC274-PolII-wt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.621813
echo ITC275-PolII-wt4.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC275-PolII-wt4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.609607
echo ITC276-PolII-DENwt1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC276-PolII-DENwt1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.715067
echo ITC277-PolII-DENwt2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC277-PolII-DENwt2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.682863
echo ITC278-PolII-AlSm1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC278-PolII-AlSm1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.800223
echo ITC279-PolII-AlSm2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC279-PolII-AlSm2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.954568
echo ITC280-PolII-DENAlSm3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC280-PolII-DENAlSm3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.898878
echo ITC281-PolII-DENAlSm4.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC281-PolII-DENAlSm4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1