#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing4794461 reads
ln -s . mm10
echo VK3R1_ColVI-unst1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R1_ColVI-unst1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.872474
echo VK3R2_ColVI-unst2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R2_ColVI-unst2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.640698
echo VK3R3_ColVI-unst3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R3_ColVI-unst3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo VK3R4_ColVI-APCst1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R4_ColVI-APCst1.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.857139
echo VK3R5_ColVI-APCst2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R5_ColVI-APCst2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.782213
echo VK3R6_ColVI-APCst3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh VK3R6_ColVI-APCst3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.846959