#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing23824156 reads
ln -s . mm10
echo GSR1-FULA1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GSR1-FULA1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.732101
echo GSR4-BULA1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GSR4-BULA1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.664926
echo GSR5-BULA2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GSR5-BULA2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.976366
echo GSR6-BELA1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GSR6-BELA1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.955158
echo GSR2-FULA1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GSR2-FULA1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.76198
echo GSR7-BELA2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GSR7-BELA2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.651049
echo GSR3-FULA3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GSR3-FULA3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.813647
echo GSR8-FUBtrachea.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GSR8-FUBtrachea.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.507501
echo GSR9-mTECsBalbc.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GSR9-mTECsBalbc.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.515239
echo GSR10-P53FllFl.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GSR10-P53FllFl.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1