#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3588162 reads
ln -s . mm10
echo GK3R99_TU1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R99_TU1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo GK3R100_TU2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R100_TU2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.802014
echo GK3R101_TU3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R101_TU3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.424341
echo GK3R102_TH1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R102_TH1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.829191
echo GK3R103_TH2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R103_TH2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.824915
echo GK3R104_TH3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R104_TH3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.857221
echo GK3R105_TR1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R105_TR1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo GK3R106_TR2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R106_TR2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.846756
echo GK3R107_TR3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R107_TR3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.673873
echo GK3R108_WU1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R108_WU1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.872805
echo GK3R109_WU2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R109_WU2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.80298
echo GK3R110_WU3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R110_WU3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.611486