#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing10791262 reads
#echo ITC118-wt1pSTAT.bam
#/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC118-wt1pSTAT.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.757401
echo ITC119-wt2pSTAT.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC119-wt2pSTAT.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.541374
echo ITC120-KO1pSTAT.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC120-KO1pSTAT.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.72732
echo ITC121-KO2pSTAT.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC121-KO2pSTAT.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.637041
echo ITC122-wt1STAT3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC122-wt1STAT3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.613646
echo ITC123-wt2STAT3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC123-wt2STAT3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.652896
echo ITC124-KO1STAT3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC124-KO1STAT3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.622526
echo ITC125-KO2STAT3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC125-KO2STAT3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.557853
echo ITC134-wt1TEAD.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC134-wt1TEAD.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.586435
echo ITC135-wt2TEAD.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC135-wt2TEAD.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.657139
echo ITC136-KO1TEAD.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC136-KO1TEAD.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.567203
echo ITC137-KO2TEAD.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC137-KO2TEAD.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.583965
echo ITC130-wt1bCAT.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC130-wt1bCAT.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.536071
echo ITC131-wt2bCAT.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC131-wt2bCAT.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.55767
echo ITC132-KO1bCAT.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC132-KO1bCAT.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.611424
echo ITC133-KO2bCAT.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC133-KO2bCAT.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.55463