#!/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 3214717
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R39-MA30.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R40-MA31.bam 5458523
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R40-MA31.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R41-MA32.bam 6261520
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R41-MA32.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R42-MA33.bam 3804843
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R42-MA33.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R43-MA34.bam 4508393
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R43-MA34.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R44-MA35.bam 4203571
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R44-MA35.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R45-MA36.bam 5293911
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R45-MA36.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R46-MA37.bam 5206951
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R46-MA37.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R47-MA38.bam 5076985
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R47-MA38.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R48-MA39.bam 2537384
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R48-MA39.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R49-MA40.bam 6834371
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R49-MA40.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R50-MA41.bam 6017056
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R50-MA41.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R51-MA42.bam 6201919
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R51-MA42.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R52-MA43.bam 4675735
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R52-MA43.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R53-MA44.bam 4912278
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R53-MA44.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R24-MA15.bam 5231656
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R24-MA15.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R25-MA16.bam 3897624
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R25-MA16.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R26-MA17.bam 3632583
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R26-MA17.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R27-MA18.bam 4175017
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R27-MA18.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R28-MA19.bam 4616506
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R28-MA19.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R29-MA20.bam 4269948
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R29-MA20.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R30-MA21.bam 5969191
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R30-MA21.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R31-MA22.bam 4953918
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R31-MA22.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R32-MA23.bam 5872956
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R32-MA23.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R33-MA24.bam 3923748
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R33-MA24.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R34-MA25.bam 4779642
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R34-MA25.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R35-MA26.bam 4139221
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R35-MA26.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R36-MA27.bam 3168895
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R36-MA27.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R37-MA28.bam 4581109
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R37-MA28.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R38-MA29.bam 4106888
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R38-MA29.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R11-MA2.bam 4019253
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R11-MA2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R12-MA3.bam 3522235
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R12-MA3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R13-MA4.bam 3620895
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R13-MA4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R14-MA5.bam 2713974
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R14-MA5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R15-MA6.bam 4654137
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R15-MA6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R16-MA7.bam 4099761
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R16-MA7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R17-MA8.bam 4310484
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R17-MA8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R18-MA9.bam 3267469
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R18-MA9.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R19-MA10.bam 3003969
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R19-MA10.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R20-MA11.bam 2525771
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R20-MA11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R21-MA12.bam 3546547
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R21-MA12.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R22-MA13.bam 3115609
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R22-MA13.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R23-MA14.bam 3709532
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R23-MA14.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R10-MA1.bam 909966
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R10-MA1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R11-MA2.bam 4019253
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R11-MA2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R12-MA3.bam 3522235
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R12-MA3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R13-MA4.bam 3620895
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R13-MA4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R14-MA5.bam 2713974
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R14-MA5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R15-MA6.bam 4654137
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R15-MA6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R16-MA7.bam 4099761
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R16-MA7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R17-MA8.bam 4310484
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R17-MA8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R18-MA9.bam 3267469
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R18-MA9.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R19-MA10.bam 3003969
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R19-MA10.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R20-MA11.bam 2525771
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R20-MA11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R21-MA12.bam 3546547
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R21-MA12.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R22-MA13.bam 3115609
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R22-MA13.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R23-MA14.bam 3709532
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R23-MA14.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R10-MA1.bam 909966
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R10-MA1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R11-MA2.bam 4609920
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R11-MA2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R12-MA3.bam 2917712
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R12-MA3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R13-MA4.bam 2861700
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R13-MA4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R14-MA5.bam 3599540
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R14-MA5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R15-MA6.bam 5293516
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R15-MA6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R16-MA7.bam 4631417
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R16-MA7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R17-MA8.bam 3263046
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R17-MA8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R18-MA9.bam 1764658
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R18-MA9.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R19-MA10.bam 2061275
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R19-MA10.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R20-MA11.bam 1194781
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R20-MA11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R21-MA12.bam 2801611
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R21-MA12.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R22-MA13.bam 2896829
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R22-MA13.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R23-MA14.bam 2951074
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R23-MA14.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R11-MA2.bam 4609920
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R11-MA2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R12-MA3.bam 2917712
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R12-MA3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R13-MA4.bam 2861700
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R13-MA4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R14-MA5.bam 3599540
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R14-MA5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R15-MA6.bam 5293516
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R15-MA6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R16-MA7.bam 4631417
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R16-MA7.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R17-MA8.bam 3263046
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R17-MA8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R18-MA9.bam 1764658
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R18-MA9.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R19-MA10.bam 2061275
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R19-MA10.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R20-MA11.bam 1194781
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R20-MA11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R21-MA12.bam 2801611
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R21-MA12.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R22-MA13.bam 2896829
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R22-MA13.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R23-MA14.bam 2951074
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R23-MA14.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo GK3R10-MA1.bam 291050
/data/results/tools/proton/tophat2unstranded-bigwig1.sh GK3R10-MA1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai