#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2345242 reads
ln -s . mm10
echo GK3R140-MU1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R140-MU1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.455944
echo GK3R141-MU2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R141-MU2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.625862
echo GK3R142-MU3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R142-MU3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.438981
echo GK3R143-MI1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R143-MI1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.515415
echo GK3R144-MI2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R144-MI2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.531463
echo GK3R145-MI3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R145-MI3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.623425
echo GK3R146-CU1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R146-CU1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.44568
echo GK3R147-CU2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R147-CU2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.503619
echo GK3R148-CU3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R148-CU3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.63549
echo GK3R149-CI1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R149-CI1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.891715
echo GK3R150-CI2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R150-CI2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.988318
echo GK3R151-CI3r.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R151-CI3r.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1