#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing 8811442 reads
ln -s . mm10
echo ITC213-wt1Me3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC213-wt1Me3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.565144
echo ITC214-wt1TCPMe3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC214-wt1TCPMe3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.507165
echo ITC215-wt3Me1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC215-wt3Me1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.971812
echo ITC216-wt3TCPMe1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC216-wt3TCPMe1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.574937
echo ITC219-SET8ko2TCPINPUT.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC219-SET8ko2TCPINPUT.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.623183
echo ITC207-wt1TCPAIC.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC207-wt1TCPAIC.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.480525
echo ITC208-wt2TCPAIC.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC208-wt2TCPAIC.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.523044
echo ITC210-SET8ko1TCPAIC.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC210-SET8ko1TCPAIC.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.641438
echo ITC211-SET8ko2TCPAIC.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC211-SET8ko2TCPAIC.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.325418
echo ITC195-wt1B1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC195-wt1B1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.502293
echo ITC196-wt2B1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC196-wt2B1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.749888
echo ITC198-wt1TCPB1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC198-wt1TCPB1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.64833
echo ITC199-wt2TCPB1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC199-wt2TCPB1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.507414
echo ITC217-wt2INPUT.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC217-wt2INPUT.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.720701
echo ITC201-SET8ko1B1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC201-SET8ko1B1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.662745
echo ITC202-SET8ko2B1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC202-SET8ko2B1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.423483
echo ITC204-wt1AIC.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC204-wt1AIC.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC205-wt2AIC.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC205-wt2AIC.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.528673
echo ITC218-wt2TCPINPUT.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC218-wt2TCPINPUT.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.54164