#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing1488048 reads
ln -s . mm10
echo IT3R49-wt1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R49-wt1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.346635
echo IT3R50-wt3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R50-wt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.402094
echo IT3R51-wt4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R51-wt4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.401622
echo IT3R52-wt6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R52-wt6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.313877
echo IT3R53-wt7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R53-wt7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.572367
echo IT3R54-ko1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R54-ko1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.254963
echo IT3R55-ko3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R55-ko3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.304101
echo IT3R56-ko4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R56-ko4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.284507
echo IT3R57-ko6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R57-ko6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.346797
echo IT3R58-ko7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R58-ko7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1