#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing1446690 reads
ln -s . mm10
echo GK3R87-GIH1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R87-GIH1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.447449
echo GK3R88-GIH2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R88-GIH2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.522714
echo GK3R89-GIH3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R89-GIH3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.435062
echo GK3R90-GIL1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R90-GIL1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.674562
echo GK3R91-GIL2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R91-GIL2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.287128
echo GK3R92-GIL3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R92-GIL3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.330964
echo GK3R93-TI1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R93-TI1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo GK3R94-TI2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R94-TI2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.789328
echo GK3R95-TI3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R95-TI3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.332946
echo GK3R96-UI1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R96-UI1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo GK3R97-UI2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R97-UI2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.273366
echo GK3R98-UI3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R98-UI3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.390101