#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3323362 reads
ln -s . mm10
echo AE3R13_L24B-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R13_L24B-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.924148
echo AE3R14_L33B-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R14_L33B-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.670273
echo AE3R15_L43B-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R15_L43B-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.619616
echo AE3R16_L59B-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R16_L59B-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.724312
echo AE3R17_L64B-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R17_L64B-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.416328
echo AE3R19_L26B-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R19_L26B-2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.616466
echo AE3R20_L29B-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R20_L29B-2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.777063
echo AE3R21_L54B-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R21_L54B-2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.34871
echo AE3R22_L58B-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R22_L58B-2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.565272
echo AE3R23_wt-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R23_wt-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo AE3R24_wt-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R24_wt-2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.783911
echo AE3R25_wt-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R25_wt-3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.621428
echo AE3R26_wtpre-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R26_wtpre-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.660633
echo AE3R27_wtpre-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R27_wtpre-2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.63852
echo AE3R28_wtpre-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R28_wtpre-3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.574686
echo AE3R29_ko-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R29_ko-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.693733
echo AE3R30_ko-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R30_ko-2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.716641
echo AE3R31_ko-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R31_ko-3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.601449
echo AE3R32_kopre-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R32_kopre-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo AE3R33_kopre-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R33_kopre-2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.800706
echo AE3R34_kopre-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AE3R34_kopre-3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.7411