#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2882421 reads
ln -s . mm10
echo GK3R131r-GFP-DARE1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R131r-GFP-DARE1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.592638
echo GK3R132r-GFP-DARE2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R132r-GFP-DARE2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.691516
echo GK3R133r-GFP-DARE3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R133r-GFP-DARE3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.716815
echo GK3R134r-TOM-DARE1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R134r-TOM-DARE1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.49139
echo GK3R135r-TOM-DARE2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R135r-TOM-DARE2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.840868
echo GK3R136r-TOM-DARE3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R136r-TOM-DARE3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.482519
echo GK3R137r-UNS-DARE1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R137r-UNS-DARE1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.589812
echo GK3R138r-UNS-DARE2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R138r-UNS-DARE2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.634715
echo GK3R139r-UNS-DARE3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R139r-UNS-DARE3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo GK3R137r-UNS-DARE1-TEST1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R137r-UNS-DARE1-TEST1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo GK3R138r-UNS-DARE2-TEST2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R138r-UNS-DARE2-TEST2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1