#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2609953 reads
ln -s . mm10
echo VK3R16_UAPC1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R16_UAPC1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.965815
echo VK3R17_UAPC2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R17_UAPC2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.975903
echo VK3R18_UAPC3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R18_UAPC3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.83992
echo VK3R19_GAPC1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R19_GAPC1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo VK3R20_GAPC2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R20_GAPC2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.908584
echo VK3R21_GAPC3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R21_GAPC3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.743151
echo VK3R22_TAPC1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R22_TAPC1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.857375
echo VK3R23_TAPC2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R23_TAPC2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.799305
echo VK3R24_TAPC3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R24_TAPC3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.660199