#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3127293 reads
ln -s . mm10
echo ITC290-Pho-wt3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC290-Pho-wt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC291-Pho-wt4.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC291-Pho-wt4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC292-Pho-DENwt1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC292-Pho-DENwt1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC293-Pho-DENwt2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC293-Pho-DENwt2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC294-Pho-AlSm1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC294-Pho-AlSm1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC295-Pho-AlSm2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC295-Pho-AlSm2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC296-Pho-DENAlSm3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC296-Pho-DENAlSm3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC297-Pho-DENAlSm4.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC297-Pho-DENAlSm4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC298-PolII-Untrwt3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC298-PolII-Untrwt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC299-PolII-Untrwt4.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC299-PolII-Untrwt4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC300-PolII-Untrko1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC300-PolII-Untrko1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC301-PolII-Untrko3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC301-PolII-Untrko3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC302-PolII-DENTCPwt1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC302-PolII-DENTCPwt1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC303-PolII-DENTCPwt3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC303-PolII-DENTCPwt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC304-PolII-DENTCPko2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC304-PolII-DENTCPko2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC305-PolII-DENTCPko4.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC305-PolII-DENTCPko4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1