#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing6226399 reads
echo ITC159-1a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC159-1a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.397137
echo ITC160-2a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC160-2a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.355348
echo ITC161-3a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC161-3a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.346653
echo ITC162-4a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC162-4a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.331387
echo ITC163-5a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC163-5a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.313245
echo ITC164-6a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC164-6a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.365818
echo ITC165-7a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC165-7a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.283849
echo ITC166-8a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC166-8a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.423788
echo ITC167-9a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC167-9a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.854632
echo ITC168-10a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC168-10a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.898544
echo ITC169-11a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC169-11a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC170-12a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC170-12a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.912363