#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing1586921 reads
ln -s . mm10
echo DK3R1r-C1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R1r-C1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.781193
echo DK3R2r-C2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R2r-C2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.765389
echo DK3R3r-C3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R3r-C3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.64124
echo DK3R4b-K23.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R4b-K23.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.774437
echo DK3R5-K2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R5-K2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.727499
echo DK3R6-K3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R6-K3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo DK3R7-C1L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R7-C1L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.618697
echo DK3R8-C2L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R8-C2L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.68503
echo DK3R9r-C3L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R9r-C3L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.7956
echo DK3R10b-K23L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R10b-K23L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.704956
echo DK3R11-K2L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R11-K2L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.71838
echo DK3R12-K3L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh DK3R12-K3L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.532429