#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing74306938 reads
ln -s . mm10
echo sortedKO21pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedKO21pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.699126
echo sortedKO22pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedKO22pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.710567
echo sortedKOIFN1pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedKOIFN1pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.678452
echo sortedKOIFN2pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedKOIFN2pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.781576
echo sortedKo01pos.sorted.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedKo01pos.sorted.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.849432
echo sortedKo02pos.sorted.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedKo02pos.sorted.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.673424
echo sortedKo1IL4pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedKo1IL4pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.68696
echo sortedKo2IL4pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedKo2IL4pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.665936
echo sortedKo61pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedKo61pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.747887
echo sortedKo62pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedKo62pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.626087
echo sortedwt01IL4pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedwt01IL4pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.749558
echo sortedwt01pos.sorted.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedwt01pos.sorted.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.94188
echo sortedwt02IL4pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedwt02IL4pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.975012
echo sortedwt02pos.sorted.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedwt02pos.sorted.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.927184
echo sortedwt21pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedwt21pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo sortedwt22pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedwt22pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.851668
echo sortedwt61pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedwt61pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.876385
echo sortedwt62pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedwt62pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.896442
echo sortedwtIFN1pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedwtIFN1pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.874837
echo sortedwtIFN2pos.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh sortedwtIFN2pos.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai 0.659379