#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing4513792 reads
ln -s . hg19
echo AE3R1_siLusi-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R1_siLusi-1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.721522
echo AE3R2_siLusi-BAF-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R2_siLusi-BAF-1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.849945
echo AE3R3_siApoA1-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R3_siApoA1-1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1
echo AE3R4_siApoA1-BAF-1.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R4_siApoA1-BAF-1.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.830666
echo AE3R5_siLusi-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R5_siLusi-2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.803989
echo AE3R6_siLusi-BAF-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R6_siLusi-BAF-2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.814175
echo AE3R7_siApoA1-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R7_siApoA1-2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.701894
echo AE3R8_siApoA1-BAF-2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R8_siApoA1-BAF-2.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.991075
echo AE3R9_siLusi-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R9_siLusi-3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.794989
echo AE3R10_siLusi-BAF-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R10_siLusi-BAF-3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.749358
echo AE3R11_siApoA1-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R11_siApoA1-3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 0.615102
echo AE3R12_siApoA1-BAF-3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig2.sh AE3R12_siApoA1-BAF-3.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1