#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2585237 reads
ln -s . mm10
echo GK3R54-MS1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R54-MS1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.891073
echo GK3R63-MS10.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R63-MS10.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.903629
echo GK3R64-MS11.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R64-MS11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.635746
echo GK3R65-MS12.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R65-MS12.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.298789
echo GK3R66-MS13.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R66-MS13.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.387197
echo GK3R67-MS14.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R67-MS14.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.767826
echo GK3R68-MS15.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R68-MS15.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.599603
echo GK3R69-MS16.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R69-MS16.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.652172
echo GK3R70-MS17.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R70-MS17.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.361316
echo GK3R71-MS18.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R71-MS18.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.563869
echo GK3R72-MS19.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R72-MS19.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.318706
echo GK3R55-MS2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R55-MS2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.594895
echo GK3R73-MS20.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R73-MS20.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.361078
echo GK3R74-MS21.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R74-MS21.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.367697
echo GK3R75-MS22.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R75-MS22.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.428442
echo GK3R76-MS23.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R76-MS23.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.595427
echo GK3R77-MS24.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R77-MS24.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.289591
echo GK3R56-MS3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R56-MS3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.519908
echo GK3R57-MS4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R57-MS4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.639994
echo GK3R58-MS5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R58-MS5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R59-MS6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R59-MS6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.786209
echo GK3R60-MS7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R60-MS7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.899848
echo GK3R61-MS8.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R61-MS8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.534489
echo GK3R62-MS9.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R62-MS9.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.758025