#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing1290149 reads
ln -s . mm10
echo IT3R35-3312-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R35-3312-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.316283
echo IT3R36-3312-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R36-3312-3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.347675
echo IT3R37-3343-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R37-3343-2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.350058
echo IT3R38-3343-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R38-3343-3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.321385
echo IT3R39-3343-4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R39-3343-4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.649797
echo IT3R40-wt1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R40-wt1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.288975
echo IT3R41-wt2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R41-wt2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.377193
echo IT3R42-wt5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R42-wt5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.917645
echo IT3R43-wt15.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R43-wt15.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.438044
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R44-wt16.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo IT3R45-wt17.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R45-wt17.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.597063
echo IT3R46-3308-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R46-3308-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.370136
echo IT3R47-3308-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R47-3308-2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo IT3R48-3308-4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R48-3308-4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.377509