#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3658897 reads
ln -s . mm10
echo SC3R1-1M14.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SC3R1-1M14.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.545258
echo SC3R2-3M14.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SC3R2-3M14.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.779469
echo SC3R3-6M14mut.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SC3R3-6M14mut.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.841045
echo SC3R4-8M14mut.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SC3R4-8M14mut.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.92979
echo SC3R5-9M14mut.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SC3R5-9M14mut.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.772581
echo SC3R6-1F16.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SC3R6-1F16.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo SC3R7-6F16.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SC3R7-6F16.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.959434
echo SC3R8-2F16mut.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SC3R8-2F16mut.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.642611
echo SC3R9-5F16mut.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SC3R9-5F16mut.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.825097
echo SC3R10-8F16mut.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SC3R10-8F16mut.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.738439