#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2233573 reads
ln -s . mm10
echo GK3R119-T1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R119-T1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.290782
echo GK3R120-T2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R120-T2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.642761
echo GK3R121-T3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R121-T3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.49522
echo GK3R122-TAm1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R122-TAm1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.525392
echo GK3R123-TAm2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R123-TAm2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.795823
echo GK3R124-TAm3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R124-TAm3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.937564
echo GK3R125-WT1H.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R125-WT1H.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.540503
echo GK3R126-WT2H.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R126-WT2H.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.631338
echo GK3R127-WT3H.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R127-WT3H.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo GK3R128-WT1R.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R128-WT1R.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.569823
echo GK3R129-WT2R.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R129-WT2R.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.731935
echo GK3R130-WT3R.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R130-WT3R.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.433223