#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing79485108 reads
ln -s . mm10
echo KO01_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh KO01_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.841986
echo KO02_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh KO02_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.67217
echo KO21_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh KO21_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.696917
echo KO22_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh KO22_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.707331
echo KO61_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh KO61_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.743861
echo KO62_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh KO62_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.621471
echo KOIFN_1_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh KOIFN_1_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.675567
echo KOIFN_2_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh KOIFN_2_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.778285
echo KOIL4_1_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh KOIL4_1_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.673441
echo KOIL4_2_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh KOIL4_2_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.653877
echo wt01_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh wt01_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.942788
echo wt02_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh wt02_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.923061
echo wt21_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh wt21_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 1
echo wt22_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh wt22_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.849914
echo wt61_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh wt61_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.866006
echo wt62_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh wt62_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.896034
echo wtIFN_1_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh wtIFN_1_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.866315
echo wtIFN_2_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh wtIFN_2_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.655132
echo wtIL4_1_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh wtIL4_1_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.732522
echo wtIL4_2_trm.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh wtIL4_2_trm.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.956661