#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3533012 reads
ln -s . mm10
echo GK3R112-Empty2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R112-Empty2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.966053
echo GK3R113-Empty3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R113-Empty3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.967698
echo GK3R114-Empty4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R114-Empty4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.859794
echo GK3R116-Wnt2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R116-Wnt2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo GK3R117-Wnt3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R117-Wnt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.995451
echo GK3R118-Wnt4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R118-Wnt4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.895244