#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing1659156 reads
ln -s . mm10
echo YK3R1-5291-4aplus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh YK3R1-5291-4aplus.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.605916
echo YK3R2-5291-4aplus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh YK3R2-5291-4aplus.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.730287
echo YK3R3-5291-4aplus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh YK3R3-5291-4aplus.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.854423
echo YK3R4-5291-4aminus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh YK3R4-5291-4aminus.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.878589
echo YK3R5-5291-4aminus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh YK3R5-5291-4aminus.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.524292
echo YK3R6-5269-4fplus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh YK3R6-5269-4fplus.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.563731
echo YK3R7-5269-4fplus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh YK3R7-5269-4fplus.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.790934
echo YK3R8-5269-4fplus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh YK3R8-5269-4fplus.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo YK3R9-5269-4fminus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh YK3R9-5269-4fminus.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.521772
echo YK3R10-5269-4fminus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh YK3R10-5269-4fminus.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.831448
echo YK3R11-Cplus-1plus.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh YK3R11-Cplus-1plus.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.638597