#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing996954 reads
ln -s . hg19
echo DSt3R1-1A-UntrPMNs.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R1-1A-UntrPMNs.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.20886
echo DSt3R2-1B-PMNsIRAplasma.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R2-1B-PMNsIRAplasma.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.0803925
echo DSt3R3-1C-PMNsIRAplasmaTIC.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R3-1C-PMNsIRAplasmaTIC.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.114441
echo DSt3R4-1D-PMNsIRAplasmaIL29.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R4-1D-PMNsIRAplasmaIL29.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.151145
echo DSt3R5-3A-UntrPMNs.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R5-3A-UntrPMNs.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.271665
echo DSt3R6-3B-PMNsIRAplasma.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R6-3B-PMNsIRAplasma.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.136236
echo DSt3R7-3C-PMNsIRAplasmaTIC.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R7-3C-PMNsIRAplasmaTIC.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.349328
echo DSt3R8-3D-PMNsIRAplasmaIL29.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R8-3D-PMNsIRAplasmaIL29.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.187489
echo DSt3R9-4A-UntrPMNs.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R9-4A-UntrPMNs.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.188481
echo DSt3R10-4B-PMNsIRAplasma.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R10-4B-PMNsIRAplasma.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.236092
echo DSt3R11-4C-PMNsIRAplasmaTIC.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R11-4C-PMNsIRAplasmaTIC.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.161628
echo DSt3R12-4D-PMNsIRAplasmaIL29.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R12-4D-PMNsIRAplasmaIL29.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.254775
echo DSt3R13-5E-UntrPMNs.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R13-5E-UntrPMNs.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.13592
echo DSt3R14-5F-PMNspolyP.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R14-5F-PMNspolyP.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.1821
echo DSt3R15-5G-PMNspolyPTIC.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R15-5G-PMNspolyPTIC.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.188001
echo DSt3R16-5H-PMNspolyPIL29.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R16-5H-PMNspolyPIL29.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.212114
echo DSt3R17-5I-PMNsTIC.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R17-5I-PMNsTIC.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.133712
echo DSt3R18-5J-PMNsIL29.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R18-5J-PMNsIL29.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.333598
echo DSt3R19-6E-UntrPMNs.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R19-6E-UntrPMNs.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.113193
echo DSt3R20-6F-PMNspolyP.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R20-6F-PMNspolyP.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.209482
echo DSt3R21-6G-PMNspolyPTIC.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R21-6G-PMNspolyPTIC.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.136615
echo DSt3R22-6H-PMNspolyPIL29.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R22-6H-PMNspolyPIL29.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.156618
echo DSt3R23-6I-PMNsTIC.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R23-6I-PMNsTIC.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.168447
echo DSt3R24-6J-PMNsIL29.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R24-6J-PMNsIL29.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.142121
echo DSt3R7-3C-PMNsIRAplasmaTIC.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R7-3C-PMNsIRAplasmaTIC.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo DSt3R29-8I-PMNsTIC.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R29-8I-PMNsTIC.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.0908065
echo DSt3R30-8J-PMNsIL29.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R30-8J-PMNsIL29.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.178226
echo DSt3R25-8E-UntrPMNs.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R25-8E-UntrPMNs.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.101767
echo DSt3R26-8F-PMNspolyP.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R26-8F-PMNspolyP.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.141666
echo DSt3R27-8G-PMNspolyPTIC.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R27-8G-PMNspolyPTIC.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.124887
echo DSt3R28-8H-PMNspolyPIL29.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh DSt3R28-8H-PMNspolyPIL29.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.0863862