#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing743223 reads
ln -s . mm10
echo ITRC27-BrEU-wt3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC27-BrEU-wt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC28-BrEU-wt4.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC28-BrEU-wt4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC29-GRO-DENTC-wt1a.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC29-GRO-DENTC-wt1a.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC30-GRO-DENTC-wt1b.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC30-GRO-DENTC-wt1b.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC31-GRO-USP22-DENTC-ko1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC31-GRO-USP22-DENTC-ko1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC32-GRO-USP22-DENTC-ko2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC32-GRO-USP22-DENTC-ko2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC33-GRO-USP22-DENTC-ko3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC33-GRO-USP22-DENTC-ko3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC34-EU-wt1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC34-EU-wt1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC35-EU-wt2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC35-EU-wt2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC36-EU-USP22-ko1.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC36-EU-USP22-ko1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC37-EU-USP22-ko2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC37-EU-USP22-ko2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC38-EU-DENTC-wt2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC38-EU-DENTC-wt2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC39-EU-DENTC-wt3.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC39-EU-DENTC-wt3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC40-EU-USP22-DENTC-ko4.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC40-EU-USP22-DENTC-ko4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITRC41-EU-USP22-DENTC-ko5.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITRC41-EU-USP22-DENTC-ko5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1