#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3702092 reads
ln -s . mm10
echo ITC274-PolII-wt3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC274-PolII-wt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC275-PolII-wt4.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC275-PolII-wt4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC276-PolII-DENwt1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC276-PolII-DENwt1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC277-PolII-DENwt2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC277-PolII-DENwt2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC278-PolII-AlSm1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC278-PolII-AlSm1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC279-PolII-AlSm2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC279-PolII-AlSm2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC280-PolII-DENAlSm3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC280-PolII-DENAlSm3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC281-PolII-DENAlSm4.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC281-PolII-DENAlSm4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC282-H2B-wt3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC282-H2B-wt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC283-H2B-wt4.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC283-H2B-wt4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC284-H2B-DENwt1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC284-H2B-DENwt1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC285-H2B-DENwt2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC285-H2B-DENwt2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC286-H2B-AlSm1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC286-H2B-AlSm1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC287-H2B-AlSm3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC287-H2B-AlSm3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC288-H2B-DENAlSm1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC288-H2B-DENAlSm1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC289-H2B-DENAlSm3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC289-H2B-DENAlSm3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1