#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing1681849 reads
ln -s . mm10
echo GK3R170-EPI1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R170-EPI1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.530965
echo GK3R171-EPI2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R171-EPI2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.894951
echo GK3R172-EPI3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R172-EPI3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo GK3R173-EPI4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R173-EPI4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.856701
echo GK3R174-EPI5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R174-EPI5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.620359
echo GK3R175-EPI6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R175-EPI6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.524351