#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing3636859 reads
echo IT3R21-5GBaM.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R21-5GBaM.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.730032

echo IT3R20-12GBF.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R20-12GBF.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.511347

echo IT3R19-8GBF.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R19-8GBF.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.56286

echo IT3R18-9GBM.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R18-9GBM.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1

echo IT3R17-1GBM.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R17-1GBM.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.58663

echo IT3R1-wt1LM.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R1-wt1LM.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.630437
#echo IT3R2-wt2LM.bam
#/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R2-wt2LM.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.536261
#echo IT3R3-wt3LM.bam
#/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R3-wt3LM.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFast#a/genome.fa.fai 0.656543
#echo IT3R4-wt4LM.bam
#/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R4-wt4LM.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.604618
#echo IT3R5-wt1LF.bam
#/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R5-wt1LF.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.81793
#echo IT3R6-wt2LF.bam
#/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R6-wt2LF.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.737567
#echo IT3R7-wt3LF.bam
#/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R7-wt3LF.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.718833
#echo IT3R8-wt4LF.bam
#/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R8-wt4LF.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.784494


echo IT3R22-3GMaF.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh IT3R22-3GMaF.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.538755