#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing12480032 reads
ln -s . mm10
echo ITC257-wt2unt.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC257-wt2unt.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.881305
echo ITC258-wt3unt.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC258-wt3unt.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.520973
echo ITC259-wt4unt.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC259-wt4unt.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.981222
echo ITC260-ko1unt.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC260-ko1unt.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC261-ko3unt.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC261-ko3unt.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.921932
echo ITC262-ko4unt.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC262-ko4unt.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.537435
echo ITC263-wt1DENTCP.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC263-wt1DENTCP.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.631127
echo ITC264-wt3DENTCP.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC264-wt3DENTCP.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.641462
echo ITC265-ko2DENTCP.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC265-ko2DENTCP.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.999045
echo ITC266-ko3DENTCP.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC266-ko3DENTCP.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.815547
echo ITC267-ko4DENTCP.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC267-ko4DENTCP.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.80452