#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2486716 reads
ln -s . mm10
echo AK3R1_A1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R1_A1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.609811
echo AK3R2_A2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R2_A2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.952928
echo AK3R3_A3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R3_A3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo AK3R4_B1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R4_B1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.541648
echo AK3R5_B2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R5_B2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.449744
echo AK3R6_B3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh AK3R6_B3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.302319
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 0.665895
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 0.481384
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 0.621185
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 0.805536
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 0.610277
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 1