python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint