#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing8732091 reads
ln -s . mm10
echo ITC243-wt3-Usp.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC243-wt3-Usp.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.49241
echo ITC244-wt4-Usp.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC244-wt4-Usp.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.742579
echo ITC245-wt1DENTCP-Usp.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC245-wt1DENTCP-Usp.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.748179
echo ITC246-wt2DENTCP-Usp.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC246-wt2DENTCP-Usp.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo ITC247-wt3DENTCP-Usp.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC247-wt3DENTCP-Usp.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.612905
echo ITC236-wt1DENTCP-H2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC236-wt1DENTCP-H2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.587577
echo ITC237-ko1DENTCP-H2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC237-ko1DENTCP-H2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.526991
echo ITC238-ko2DENTCP-H2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC238-ko2DENTCP-H2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.270968
echo ITC239-Tg1-H2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC239-Tg1-H2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.373292
echo ITC240-Tg2-H2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC240-Tg2-H2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.437609
echo ITC241-Tg3-H2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC241-Tg3-H2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.429019
echo ITC242-Tg4-H2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC242-Tg4-H2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.361632
echo ITC232-wt3-H2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC232-wt3-H2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.423083
echo ITC233-wt4-H2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC233-wt4-H2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.364107
echo ITC234-ko2-H2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC234-ko2-H2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.455731
echo ITC235-ko3-H2.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC235-ko3-H2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.463699