#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2917559 reads
ln -s . hg19
echo PH3R16-Ldc10-Ctrl3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R16-Ldc10-Ctrl3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.688119
echo PH3R17-Ldc10-Ig3-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R17-Ldc10-Ig3-1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.806021
echo PH3R18-Ldc10-Ig3-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R18-Ldc10-Ig3-2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.667317
echo PH3R19-Ldc10-Ig3-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R19-Ldc10-Ig3-3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.689464
echo PH3R20-Ldc10-Ig4-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R20-Ldc10-Ig4-1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.608914
echo PH3R21-Ldc10-Ig4-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R21-Ldc10-Ig4-2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.779966
echo PH3R22-Ldc10-Ig4-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R22-Ldc10-Ig4-3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.679347
echo PH3R8-Con1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R8-Con1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.8865
echo PH3R9-Con2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R9-Con2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.737384
echo PH3R10-Con3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R10-Con3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.647349
echo PH3R11-Dox1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R11-Dox1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.728793
echo PH3R12-Dox2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R12-Dox2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.944955
echo PH3R13-Dox3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R13-Dox3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo PH3R14-Ldc10-Ctrl1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R14-Ldc10-Ctrl1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.789017
echo PH3R15-Ldc10-Ctrl2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh PH3R15-Ldc10-Ctrl2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.630746