#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2999 reads
ln -s . hg19
echo PH3R1-neg1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R1-neg1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R2-neg2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R2-neg2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R3-neg3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R3-neg3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R4-Ig3-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R4-Ig3-1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R5-Ig3-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R5-Ig3-2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R6-Ig3-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R6-Ig3-3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R-neg1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R-neg1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R-neg2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R-neg2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R-neg3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R-neg3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R-Ig3-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R-Ig3-1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R-Ig3-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R-Ig3-2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R-Ig3-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R-Ig3-3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1