#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3087031 reads
ln -s . mm10
echo AK3R7_C1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R7_C1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.826648
echo AK3R8_C2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R8_C2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.597595
echo AK3R9_C3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R9_C3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.771144
echo AK3R10_D1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R10_D1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo AK3R11_D2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R11_D2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.757603
echo AK3R12_D3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R12_D3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.826648