#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing291050 reads
ln -s . mm10
echo GK3R39-MA30.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R39-MA30.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R40-MA31.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R40-MA31.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R41-MA32.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R41-MA32.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R42-MA33.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R42-MA33.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R43-MA34.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R43-MA34.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R44-MA35.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R44-MA35.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R45-MA36.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R45-MA36.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R46-MA37.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R46-MA37.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R47-MA38.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R47-MA38.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R48-MA39.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R48-MA39.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R49-MA40.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R49-MA40.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R50-MA41.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R50-MA41.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R51-MA42.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R51-MA42.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R52-MA43.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R52-MA43.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R53-MA44.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R53-MA44.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R24-MA15.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R24-MA15.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R25-MA16.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R25-MA16.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R26-MA17.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R26-MA17.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R27-MA18.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R27-MA18.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R28-MA19.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R28-MA19.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R29-MA20.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R29-MA20.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R30-MA21.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R30-MA21.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R31-MA22.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R31-MA22.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R32-MA23.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R32-MA23.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R33-MA24.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R33-MA24.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R34-MA25.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R34-MA25.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R35-MA26.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R35-MA26.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R36-MA27.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R36-MA27.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R37-MA28.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R37-MA28.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R38-MA29.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R38-MA29.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R11-MA2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R11-MA2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R12-MA3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R12-MA3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R13-MA4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R13-MA4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R14-MA5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R14-MA5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R15-MA6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R15-MA6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R16-MA7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R16-MA7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R17-MA8.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R17-MA8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R18-MA9.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R18-MA9.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R19-MA10.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R19-MA10.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R20-MA11.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R20-MA11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R21-MA12.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R21-MA12.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R22-MA13.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R22-MA13.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R23-MA14.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R23-MA14.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R10-MA1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R10-MA1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R11-MA2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R11-MA2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R12-MA3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R12-MA3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R13-MA4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R13-MA4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R14-MA5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R14-MA5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R15-MA6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R15-MA6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R16-MA7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R16-MA7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R17-MA8.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R17-MA8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R18-MA9.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R18-MA9.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R19-MA10.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R19-MA10.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R20-MA11.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R20-MA11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R21-MA12.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R21-MA12.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R22-MA13.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R22-MA13.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R23-MA14.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R23-MA14.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R10-MA1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R10-MA1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R11-MA2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R11-MA2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R12-MA3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R12-MA3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R13-MA4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R13-MA4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R14-MA5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R14-MA5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R15-MA6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R15-MA6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R16-MA7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R16-MA7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R17-MA8.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R17-MA8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R18-MA9.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R18-MA9.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R19-MA10.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R19-MA10.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R20-MA11.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R20-MA11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R21-MA12.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R21-MA12.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R22-MA13.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R22-MA13.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R23-MA14.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R23-MA14.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R11-MA2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R11-MA2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R12-MA3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R12-MA3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R13-MA4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R13-MA4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R14-MA5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R14-MA5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R15-MA6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R15-MA6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R16-MA7.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R16-MA7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R17-MA8.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R17-MA8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R18-MA9.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R18-MA9.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R19-MA10.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R19-MA10.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R20-MA11.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R20-MA11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R21-MA12.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R21-MA12.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R22-MA13.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R22-MA13.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R23-MA14.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R23-MA14.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo GK3R10-MA1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh GK3R10-MA1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1