#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2884541 reads
ln -s . mm10
echo mergedDK3R10b-K23L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R10b-K23L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.676902
echo mergedDK3R11-K2L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R11-K2L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.641219
echo mergedDK3R12-K3L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R12-K3L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.490242
echo mergedDK3R1r-C1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R1r-C1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.738733
echo mergedDK3R2r-C2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R2r-C2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.757495
echo mergedDK3R3r-C3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R3r-C3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.586366
echo mergedDK3R4b-K23.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R4b-K23.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.85064
echo mergedDK3R5-K2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R5-K2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.710072
echo mergedDK3R6-K3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R6-K3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo mergedDK3R7-C1L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R7-C1L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.752105
echo mergedDK3R8-C2L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R8-C2L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.680676
echo mergedDK3R9r-C3L4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh mergedDK3R9r-C3L4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.758094