python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L482-Diamide-0min-Input/L482-Diamide-0min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L482-Diamide-0min-Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L483-Diamide-0min-Pol2/L483-Diamide-0min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L483-Diamide-0min-Pol2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L484-Diamide-0min-Pol2pS2/L484-Diamide-0min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L484-Diamide-0min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L485-Diamide-0min-V5_Input/L485-Diamide-0min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L485-Diamide-0min-V5_Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L486-Diamide-0min-V5_HSF1/L486-Diamide-0min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L486-Diamide-0min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L487-Diamide-30min-Input/L487-Diamide-30min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L487-Diamide-30min-Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L488-Diamide-30min-Pol2/L488-Diamide-30min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L488-Diamide-30min-Pol2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L489-Diamide-30min-Pol2pS2/L489-Diamide-30min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L489-Diamide-30min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L490-Diamide-30min-V5_Input/L490-Diamide-30min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L490-Diamide-30min-V5_Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L491-Diamide-30min-V5_HSF1/L491-Diamide-30min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L491-Diamide-30min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L492-Diamide-60min-Input/L492-Diamide-60min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L492-Diamide-60min-Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L493-Diamide-60min-Pol2/L493-Diamide-60min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L493-Diamide-60min-Pol2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L494-Diamide-60min-Pol2pS2/L494-Diamide-60min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L494-Diamide-60min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L495-Diamide-60min-V5_Input/L495-Diamide-60min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L495-Diamide-60min-V5_Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L496-Diamide-60min-V5_HSF1/L496-Diamide-60min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L496-Diamide-60min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L482-Diamide-0min-Input/L482-Diamide-0min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L482-Diamide-0min-Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L483-Diamide-0min-Pol2/L483-Diamide-0min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L483-Diamide-0min-Pol2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L484-Diamide-0min-Pol2pS2/L484-Diamide-0min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L484-Diamide-0min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L485-Diamide-0min-V5_Input/L485-Diamide-0min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L485-Diamide-0min-V5_Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L486-Diamide-0min-V5_HSF1/L486-Diamide-0min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L486-Diamide-0min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L487-Diamide-30min-Input/L487-Diamide-30min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L487-Diamide-30min-Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L488-Diamide-30min-Pol2/L488-Diamide-30min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L488-Diamide-30min-Pol2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L489-Diamide-30min-Pol2pS2/L489-Diamide-30min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L489-Diamide-30min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L490-Diamide-30min-V5_Input/L490-Diamide-30min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L490-Diamide-30min-V5_Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L491-Diamide-30min-V5_HSF1/L491-Diamide-30min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L491-Diamide-30min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L492-Diamide-60min-Input/L492-Diamide-60min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L492-Diamide-60min-Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L493-Diamide-60min-Pol2/L493-Diamide-60min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L493-Diamide-60min-Pol2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L494-Diamide-60min-Pol2pS2/L494-Diamide-60min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L494-Diamide-60min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L495-Diamide-60min-V5_Input/L495-Diamide-60min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L495-Diamide-60min-V5_Input.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L496-Diamide-60min-V5_HSF1/L496-Diamide-60min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L496-Diamide-60min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPM -RPM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L482-Diamide-0min-Input/L482-Diamide-0min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L482-Diamide-0min-Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L483-Diamide-0min-Pol2/L483-Diamide-0min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L483-Diamide-0min-Pol2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L484-Diamide-0min-Pol2pS2/L484-Diamide-0min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L484-Diamide-0min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L485-Diamide-0min-V5_Input/L485-Diamide-0min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L485-Diamide-0min-V5_Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L486-Diamide-0min-V5_HSF1/L486-Diamide-0min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L486-Diamide-0min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L487-Diamide-30min-Input/L487-Diamide-30min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L487-Diamide-30min-Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L488-Diamide-30min-Pol2/L488-Diamide-30min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L488-Diamide-30min-Pol2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L489-Diamide-30min-Pol2pS2/L489-Diamide-30min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L489-Diamide-30min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L490-Diamide-30min-V5_Input/L490-Diamide-30min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L490-Diamide-30min-V5_Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L491-Diamide-30min-V5_HSF1/L491-Diamide-30min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L491-Diamide-30min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L492-Diamide-60min-Input/L492-Diamide-60min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L492-Diamide-60min-Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L493-Diamide-60min-Pol2/L493-Diamide-60min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L493-Diamide-60min-Pol2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L494-Diamide-60min-Pol2pS2/L494-Diamide-60min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L494-Diamide-60min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L495-Diamide-60min-V5_Input/L495-Diamide-60min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L495-Diamide-60min-V5_Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes.500bp_ext 0 ~/ENCODE4/datasets-ChIP/L496-Diamide-60min-V5_HSF1/L496-Diamide-60min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.500bp_ext.L496-Diamide-60min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L482-Diamide-0min-Input/L482-Diamide-0min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L482-Diamide-0min-Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L483-Diamide-0min-Pol2/L483-Diamide-0min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L483-Diamide-0min-Pol2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L484-Diamide-0min-Pol2pS2/L484-Diamide-0min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L484-Diamide-0min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L485-Diamide-0min-V5_Input/L485-Diamide-0min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L485-Diamide-0min-V5_Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L486-Diamide-0min-V5_HSF1/L486-Diamide-0min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L486-Diamide-0min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L487-Diamide-30min-Input/L487-Diamide-30min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L487-Diamide-30min-Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L488-Diamide-30min-Pol2/L488-Diamide-30min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L488-Diamide-30min-Pol2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L489-Diamide-30min-Pol2pS2/L489-Diamide-30min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L489-Diamide-30min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L490-Diamide-30min-V5_Input/L490-Diamide-30min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L490-Diamide-30min-V5_Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L491-Diamide-30min-V5_HSF1/L491-Diamide-30min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L491-Diamide-30min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L492-Diamide-60min-Input/L492-Diamide-60min-Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L492-Diamide-60min-Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L493-Diamide-60min-Pol2/L493-Diamide-60min-Pol2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L493-Diamide-60min-Pol2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L494-Diamide-60min-Pol2pS2/L494-Diamide-60min-Pol2pS2.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L494-Diamide-60min-Pol2pS2.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L495-Diamide-60min-V5_Input/L495-Diamide-60min-V5_Input.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L495-Diamide-60min-V5_Input.2x36mers.sacCer3.unique.dedup.RPKM &
python ~/code/bedRPKMfromBAM.py ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.genes 0 ~/ENCODE4/datasets-ChIP/L496-Diamide-60min-V5_HSF1/L496-Diamide-60min-V5_HSF1.2x36mers.sacCer3.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes genes.L496-Diamide-60min-V5_HSF1.2x36mers.sacCer3.unique.dedup.RPKM &