#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing10791262 reads
echo ITC126-wt1YAP.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC126-wt1YAP.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.706224
echo ITC127-wt2YAP.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC127-wt2YAP.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.54196
echo ITC128-KO1YAP.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC128-KO1YAP.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC129-KO2YAP.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC129-KO2YAP.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.665145
echo ITC138-wt1TAZ.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC138-wt1TAZ.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.654354
echo ITC139-wt2TAZ.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC139-wt2TAZ.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.567924
echo ITC140-KO1TAZ.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC140-KO1TAZ.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.565124
echo ITC141-KO2TAZ.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC141-KO2TAZ.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.471708
echo ITC114-wt1Input.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC114-wt1Input.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.642407
echo ITC115-wt2Input.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC115-wt2Input.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.682569
echo ITC116-KO1Input.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC116-KO1Input.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.591918
echo ITC117-KO2Input.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC117-KO2Input.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.536294