#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2708589 reads
ln -s . mm10
echo GK3R78-UDS1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R78-UDS1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.653505
echo GK3R79-UDS2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R79-UDS2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.725048
echo GK3R80-UDS3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R80-UDS3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.698569
echo GK3R81-TDS1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R81-TDS1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.826169
echo GK3R82-TDS2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R82-TDS2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.73475
echo GK3R83-TDS3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R83-TDS3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.783879
echo GK3R84-GDS1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R84-GDS1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.873025
echo GK3R85-GDS2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R85-GDS2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R86-GDS3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R86-GDS3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.814249