#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing7240101 reads
ln -s . mm10
echo MF3R1_Prox1-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh MF3R1_Prox1-1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.771067
echo MF3R2_Prox1-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh MF3R2_Prox1-2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.88766
echo MF3R3_Prox1-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh MF3R3_Prox1-3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.859976
echo MF3R4_GFP1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh MF3R4_GFP1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo MF3R5_GFP2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh MF3R5_GFP2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.653788
echo MF3R6_GFP3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh MF3R6_GFP3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.483503