#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3726420 reads
ln -s . mm10
echo GK3R161-ColVICreLtbR-L10.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R161-ColVICreLtbR-L10.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.498769
echo GK3R162-ColVICreLtbR-L11.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R162-ColVICreLtbR-L11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.654678
echo GK3R163-ColVICreLtbR-L12.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R163-ColVICreLtbR-L12r.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo GK3R153-Wt-W2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R153-Wt-W2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.644385
echo GK3R154-Wt-W3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R154-Wt-W3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo GK3R155-TnfR1-D4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R155-TnfR1-D4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.595716
echo GK3R156-TnfR1-D5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R156-TnfR1-D5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.635101
echo GK3R157-TnfR1-D6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R157-TnfR1-D6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.40701
echo GK3R158-ColVICreTnfR1-T7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R158-ColVICreTnfR1-T7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.520041
echo GK3R159-ColVICreTnfR1-T8.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R159-ColVICreTnfR1-T8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.389391
echo GK3R160-ColVICreTnfR1-T9.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R160-ColVICreTnfR1-T9.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.64373
echo GK3R152-Wt-W1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R152-Wt-W1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.533108