#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2841416 reads
ln -s . mm10
echo GK3R164-CL1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R164-CL1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.475308
echo GK3R165-CL2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R165-CL2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.558658
echo GK3R166-CL3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R166-CL3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.637349
echo GK3R167-ML1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R167-ML1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.588752
echo GK3R168-ML2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R168-ML2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.530314
echo GK3R169-ML3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R169-ML3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1