#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3767739 reads
echo GK3R1-T1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R1-T1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.811281
echo GK3R2-T2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R2-T2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.877861
echo GK3R3-T3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R3-T3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.953107
echo GK3R4-U1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R4-U1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.948969
echo GK3R6-U3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R6-U3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R7-G1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R7-G1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.762508
echo GK3R8-G2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R8-G2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.752345
echo GK3R9-G3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R9-G3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.365795
echo GK3R5-U2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R5-U2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.738327