#!/bin/bash
# Sampling to smallest library containing 10,094,538 reads
ln -s ../bowtie2_001/sort_uniq.bam ITC92-ctrlCh1.bam	     
ln -s ../bowtie2_002/sort_uniq.bam ITC93-ctrlCh2.bam	     
ln -s ../bowtie2_003/sort_uniq.bam ITC90-ctrlCh1-Input.bam
ln -s ../bowtie2_004/sort_uniq.bam ITC91-ctrlCh2-Input.bam


/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC93-ctrlCh2.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.588235
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC92-ctrlCh1.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.37037
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC90-ctrlCh1-Input.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 1
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC91-ctrlCh2-Input.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 1