python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.1x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.1x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.1x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.1x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.1x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L01_exp190220_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.1x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.1x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L01_exp190220_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L01_exp190220_MK555_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.1x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.1x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.1x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.1x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.1x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L03_exp190220_MK645_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.1x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.1x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L03_exp190220_MK645_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L03_exp190220_MK645_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.1x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.1x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.1x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.1x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.1x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L04_exp190220_MK653_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.1x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.1x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L04_exp190220_MK653_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L04_exp190220_MK653_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.1x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.1x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.1x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.1x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.1x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L05_exp190220_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.1x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.1x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L05_exp190220_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L05_exp190220_MK554_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.1x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.1x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.1x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.1x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.1x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L06_exp190221_MK637_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.1x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.1x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L06_exp190221_MK637_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L06_exp190221_MK637_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.1x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.1x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.1x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.1x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.1x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190429L07_exp190221_MK627_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.1x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.1x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190429L07_exp190221_MK627_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190429L07_exp190221_MK627_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L65_MS521_SCEG_AB101.1x36mers.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 190722L65_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L65_MS521_SCEG_AB101.1x36mers.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 190722L65_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L65_MS521_SCEG_AB101.1x36mers.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 190722L65_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L65_MS521_SCEG_AB101.1x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L65_MS521_SCEG_AB101.1x36mers.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 190722L65_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L65_MS521_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L65_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L65_MS521_SCEG_AB101.1x36mers.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 190722L65_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L65_MS521_SCEG_AB101.1x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L65_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L65_MS521_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L66_MS529_SCEG_AB101.1x36mers.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 190722L66_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L66_MS529_SCEG_AB101.1x36mers.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 190722L66_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L66_MS529_SCEG_AB101.1x36mers.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 190722L66_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L66_MS529_SCEG_AB101.1x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L66_MS529_SCEG_AB101.1x36mers.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 190722L66_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L66_MS529_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L66_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L66_MS529_SCEG_AB101.1x36mers.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 190722L66_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L66_MS529_SCEG_AB101.1x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L66_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L66_MS529_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L67_MS527_SCEG_AB101.1x36mers.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 190722L67_MS527_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L67_MS527_SCEG_AB101.1x36mers.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 190722L67_MS527_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L67_MS527_SCEG_AB101.1x36mers.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 190722L67_MS527_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L67_MS527_SCEG_AB101.1x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L67_MS527_SCEG_AB101.1x36mers.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 190722L67_MS527_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L67_MS527_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L67_MS527_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L67_MS527_SCEG_AB101.1x36mers.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 190722L67_MS527_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L67_MS527_SCEG_AB101.1x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L67_MS527_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L67_MS527_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L68_MS522_SCEG_AB101.1x36mers.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 190722L68_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L68_MS522_SCEG_AB101.1x36mers.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 190722L68_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L68_MS522_SCEG_AB101.1x36mers.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 190722L68_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L68_MS522_SCEG_AB101.1x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L68_MS522_SCEG_AB101.1x36mers.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 190722L68_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L68_MS522_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L68_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L68_MS522_SCEG_AB101.1x36mers.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 190722L68_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L68_MS522_SCEG_AB101.1x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L68_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L68_MS522_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L69_MS524_SCEG_AB101.1x36mers.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 190722L69_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L69_MS524_SCEG_AB101.1x36mers.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 190722L69_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L69_MS524_SCEG_AB101.1x36mers.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 190722L69_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L69_MS524_SCEG_AB101.1x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L69_MS524_SCEG_AB101.1x36mers.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 190722L69_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L69_MS524_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L69_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L69_MS524_SCEG_AB101.1x36mers.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 190722L69_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L69_MS524_SCEG_AB101.1x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L69_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L69_MS524_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L70_MS528_SCEG_AB101.1x36mers.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 190722L70_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L70_MS528_SCEG_AB101.1x36mers.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 190722L70_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L70_MS528_SCEG_AB101.1x36mers.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 190722L70_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L70_MS528_SCEG_AB101.1x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L70_MS528_SCEG_AB101.1x36mers.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 190722L70_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L70_MS528_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L70_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L70_MS528_SCEG_AB101.1x36mers.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 190722L70_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L70_MS528_SCEG_AB101.1x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L70_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L70_MS528_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L71_MS523_SCEG_AB101.1x36mers.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 190722L71_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L71_MS523_SCEG_AB101.1x36mers.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 190722L71_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L71_MS523_SCEG_AB101.1x36mers.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 190722L71_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L71_MS523_SCEG_AB101.1x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L71_MS523_SCEG_AB101.1x36mers.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 190722L71_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L71_MS523_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 190722L71_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L71_MS523_SCEG_AB101.1x36mers.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 190722L71_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L71_MS523_SCEG_AB101.1x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 190722L71_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.190722L71_MS523_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.1x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.1x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.1x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.1x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.1x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L02_exp190916_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.1x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.1x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L02_exp190916_MK555_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L02_exp190916_MK555_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.1x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.1x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.1x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.1x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.1x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L03_exp190918_MK582_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.1x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.1x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L03_exp190918_MK582_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L03_exp190918_MK582_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.1x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.1x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.1x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.1x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.1x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L04_exp190920_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.1x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.1x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L04_exp190920_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L04_exp190920_MK820_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.1x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.1x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.1x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.1x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.1x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L05_exp190918_MK532_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.1x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.1x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L05_exp190918_MK532_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L05_exp190918_MK532_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.1x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.1x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.1x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.1x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.1x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L06_exp190916_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.1x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.1x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L06_exp190916_MK554_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L06_exp190916_MK554_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.1x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.1x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.1x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.1x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.1x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191002L08_exp190916_MK812_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.1x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.1x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191002L08_exp190916_MK812_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191002L08_exp190916_MK812_SCEG_AB101.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L01_MS534_SCEG_AB107.1x36mers.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 191113L01_MS534_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L01_MS534_SCEG_AB107.1x36mers.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 191113L01_MS534_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L01_MS534_SCEG_AB107.1x36mers.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 191113L01_MS534_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L01_MS534_SCEG_AB107.1x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L01_MS534_SCEG_AB107.1x36mers.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 191113L01_MS534_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L01_MS534_SCEG_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L01_MS534_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L01_MS534_SCEG_AB107.1x36mers.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 191113L01_MS534_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L01_MS534_SCEG_AB107.1x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L01_MS534_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L01_MS534_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L02_MS535_SCEG_AB107.1x36mers.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 191113L02_MS535_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L02_MS535_SCEG_AB107.1x36mers.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 191113L02_MS535_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L02_MS535_SCEG_AB107.1x36mers.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 191113L02_MS535_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L02_MS535_SCEG_AB107.1x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L02_MS535_SCEG_AB107.1x36mers.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 191113L02_MS535_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L02_MS535_SCEG_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L02_MS535_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L02_MS535_SCEG_AB107.1x36mers.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 191113L02_MS535_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L02_MS535_SCEG_AB107.1x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L02_MS535_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L02_MS535_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L03_MS536c1_SCEG_AB107.1x36mers.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 191113L03_MS536c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L03_MS536c1_SCEG_AB107.1x36mers.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 191113L03_MS536c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L03_MS536c1_SCEG_AB107.1x36mers.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 191113L03_MS536c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L03_MS536c1_SCEG_AB107.1x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L03_MS536c1_SCEG_AB107.1x36mers.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 191113L03_MS536c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L03_MS536c1_SCEG_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L03_MS536c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L03_MS536c1_SCEG_AB107.1x36mers.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 191113L03_MS536c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L03_MS536c1_SCEG_AB107.1x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L03_MS536c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L03_MS536c1_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L04_MS536c2_SCEG_AB107.1x36mers.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 191113L04_MS536c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L04_MS536c2_SCEG_AB107.1x36mers.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 191113L04_MS536c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L04_MS536c2_SCEG_AB107.1x36mers.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 191113L04_MS536c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L04_MS536c2_SCEG_AB107.1x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L04_MS536c2_SCEG_AB107.1x36mers.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 191113L04_MS536c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L04_MS536c2_SCEG_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L04_MS536c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L04_MS536c2_SCEG_AB107.1x36mers.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 191113L04_MS536c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L04_MS536c2_SCEG_AB107.1x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L04_MS536c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L04_MS536c2_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L05_MS537c1_SCEG_AB107.1x36mers.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 191113L05_MS537c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L05_MS537c1_SCEG_AB107.1x36mers.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 191113L05_MS537c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L05_MS537c1_SCEG_AB107.1x36mers.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 191113L05_MS537c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L05_MS537c1_SCEG_AB107.1x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L05_MS537c1_SCEG_AB107.1x36mers.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 191113L05_MS537c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L05_MS537c1_SCEG_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L05_MS537c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L05_MS537c1_SCEG_AB107.1x36mers.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 191113L05_MS537c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L05_MS537c1_SCEG_AB107.1x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L05_MS537c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L05_MS537c1_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L06_MS537c2_SCEG_AB107.1x36mers.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 191113L06_MS537c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L06_MS537c2_SCEG_AB107.1x36mers.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 191113L06_MS537c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L06_MS537c2_SCEG_AB107.1x36mers.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 191113L06_MS537c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L06_MS537c2_SCEG_AB107.1x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L06_MS537c2_SCEG_AB107.1x36mers.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 191113L06_MS537c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L06_MS537c2_SCEG_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L06_MS537c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L06_MS537c2_SCEG_AB107.1x36mers.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 191113L06_MS537c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L06_MS537c2_SCEG_AB107.1x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L06_MS537c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L06_MS537c2_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L07_MS538c1_SCEG_AB107.1x36mers.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 191113L07_MS538c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L07_MS538c1_SCEG_AB107.1x36mers.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 191113L07_MS538c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L07_MS538c1_SCEG_AB107.1x36mers.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 191113L07_MS538c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L07_MS538c1_SCEG_AB107.1x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L07_MS538c1_SCEG_AB107.1x36mers.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 191113L07_MS538c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L07_MS538c1_SCEG_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L07_MS538c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L07_MS538c1_SCEG_AB107.1x36mers.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 191113L07_MS538c1_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L07_MS538c1_SCEG_AB107.1x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L07_MS538c1_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L07_MS538c1_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L08_MS538c2_SCEG_AB107.1x36mers.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 191113L08_MS538c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L08_MS538c2_SCEG_AB107.1x36mers.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 191113L08_MS538c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L08_MS538c2_SCEG_AB107.1x36mers.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 191113L08_MS538c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L08_MS538c2_SCEG_AB107.1x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L08_MS538c2_SCEG_AB107.1x36mers.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 191113L08_MS538c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L08_MS538c2_SCEG_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191113L08_MS538c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L08_MS538c2_SCEG_AB107.1x36mers.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 191113L08_MS538c2_SCEG_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L08_MS538c2_SCEG_AB107.1x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191113L08_MS538c2_SCEG_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191113L08_MS538c2_SCEG_AB107.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.1x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.191127L01_exp1911_MK554_SCEG_alpha-factor_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L49_MS521_SCEG_AB101.1x36mers.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 200218L49_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L49_MS521_SCEG_AB101.1x36mers.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 200218L49_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L49_MS521_SCEG_AB101.1x36mers.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 200218L49_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L49_MS521_SCEG_AB101.1x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L49_MS521_SCEG_AB101.1x36mers.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 200218L49_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L49_MS521_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L49_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L49_MS521_SCEG_AB101.1x36mers.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 200218L49_MS521_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L49_MS521_SCEG_AB101.1x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L49_MS521_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L49_MS521_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L50_MS522_SCEG_AB101.1x36mers.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 200218L50_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L50_MS522_SCEG_AB101.1x36mers.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 200218L50_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L50_MS522_SCEG_AB101.1x36mers.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 200218L50_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L50_MS522_SCEG_AB101.1x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L50_MS522_SCEG_AB101.1x36mers.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 200218L50_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L50_MS522_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L50_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L50_MS522_SCEG_AB101.1x36mers.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 200218L50_MS522_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L50_MS522_SCEG_AB101.1x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L50_MS522_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L50_MS522_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L51_MS523_SCEG_AB101.1x36mers.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 200218L51_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L51_MS523_SCEG_AB101.1x36mers.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 200218L51_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L51_MS523_SCEG_AB101.1x36mers.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 200218L51_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L51_MS523_SCEG_AB101.1x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L51_MS523_SCEG_AB101.1x36mers.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 200218L51_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L51_MS523_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L51_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L51_MS523_SCEG_AB101.1x36mers.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 200218L51_MS523_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L51_MS523_SCEG_AB101.1x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L51_MS523_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L51_MS523_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L52_MS524_SCEG_AB101.1x36mers.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 200218L52_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L52_MS524_SCEG_AB101.1x36mers.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 200218L52_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L52_MS524_SCEG_AB101.1x36mers.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 200218L52_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L52_MS524_SCEG_AB101.1x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L52_MS524_SCEG_AB101.1x36mers.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 200218L52_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L52_MS524_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L52_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L52_MS524_SCEG_AB101.1x36mers.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 200218L52_MS524_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L52_MS524_SCEG_AB101.1x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L52_MS524_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L52_MS524_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L53_MS528_SCEG_AB101.1x36mers.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 200218L53_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L53_MS528_SCEG_AB101.1x36mers.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 200218L53_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L53_MS528_SCEG_AB101.1x36mers.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 200218L53_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L53_MS528_SCEG_AB101.1x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L53_MS528_SCEG_AB101.1x36mers.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 200218L53_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L53_MS528_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L53_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L53_MS528_SCEG_AB101.1x36mers.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 200218L53_MS528_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L53_MS528_SCEG_AB101.1x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L53_MS528_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L53_MS528_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L54_MS529_SCEG_AB101.1x36mers.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 200218L54_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L54_MS529_SCEG_AB101.1x36mers.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 200218L54_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L54_MS529_SCEG_AB101.1x36mers.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 200218L54_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L54_MS529_SCEG_AB101.1x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L54_MS529_SCEG_AB101.1x36mers.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 200218L54_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L54_MS529_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L54_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L54_MS529_SCEG_AB101.1x36mers.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 200218L54_MS529_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L54_MS529_SCEG_AB101.1x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L54_MS529_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L54_MS529_SCEG_AB101.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.1x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L55_exp200115_MK846_SCD_G1_DMSO_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.1x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L56_exp200115_MK846_SCD_G1_CMK_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.1x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L57_exp200115_MK846_SCD_G1_RAPA_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.1x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L58_exp200115_MK846_SCD_G1_RAPA_CMK_AB01.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.1x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L59_exp200115_MK846_SCD_G1_DMSO_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.1x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L60_exp200115_MK846_SCD_G1_CMK_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.1x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L61_exp200115_MK846_SCD_G1_RAPA_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.1x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200218L62_exp200115_MK846_SCD_G1_RAPA_CMK_AB107.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.1x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.1x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.1x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.1x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.1x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200526L73_exp2005_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.1x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.1x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200526L73_exp2005_MK820_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200526L73_exp2005_MK820_SCEG_AB101.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.1x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L10_exp200625_MK846_SCD_RAPA-30min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.1x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L11_exp200625_MK846_SCD_CMK-02.5min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.1x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L12_exp200625_MK846_SCD_CMK-05min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.1x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200709L13_exp200625_MK846_SCD_CMK-15min_AB107.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L25_MK689_SCEG_AB101.1x36mers.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 200808L25_MK689_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L25_MK689_SCEG_AB101.1x36mers.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 200808L25_MK689_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L25_MK689_SCEG_AB101.1x36mers.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 200808L25_MK689_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L25_MK689_SCEG_AB101.1x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L25_MK689_SCEG_AB101.1x36mers.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 200808L25_MK689_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L25_MK689_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200808L25_MK689_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L25_MK689_SCEG_AB101.1x36mers.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 200808L25_MK689_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L25_MK689_SCEG_AB101.1x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L25_MK689_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L25_MK689_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L26_MK711_SCEG_AB101.1x36mers.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 200808L26_MK711_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L26_MK711_SCEG_AB101.1x36mers.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 200808L26_MK711_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L26_MK711_SCEG_AB101.1x36mers.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 200808L26_MK711_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L26_MK711_SCEG_AB101.1x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L26_MK711_SCEG_AB101.1x36mers.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 200808L26_MK711_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L26_MK711_SCEG_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200808L26_MK711_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L26_MK711_SCEG_AB101.1x36mers.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 200808L26_MK711_SCEG_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L26_MK711_SCEG_AB101.1x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200808L26_MK711_SCEG_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200808L26_MK711_SCEG_AB101.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.1x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L01_exp200916_MK918_SCD_DMSO_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.1x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.1x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.1x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.1x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L05_exp200917_MK919_SCD_DMSO_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-00min-control_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.1x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L06_exp200917_MK919_SCD_CMK-01min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.1x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L07_exp200917_MK919_SCD_CMK-03min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.1x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.200925L08_exp200917_MK919_SCD_CMK-10min_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.1x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L01_exp201103_MK918_SCD_DMSO_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.1x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.1x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L05_exp201104_MK978_SCD_DMSO_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.1x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L08_exp201105_MK893_SCD_DMSO_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.1x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L09_exp201105_MK893_SCD_RAPA-30min_AB107.2x36mers.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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L10_exp200916_MK918_SCD_DMSO_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L11_exp200916_MK918_SCD_1NMPP1-01min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L12_exp200916_MK918_SCD_1NMPP1-03min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L13_exp200916_MK918_SCD_1NMPP1-10min_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L14_exp201103_MK918_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L14_exp201103_MK918_SCD_DMSO_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L15_exp201103_MK918_SCD_1NMPP1-01min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L16_exp201103_MK918_SCD_1NMPP1-03min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L17_exp201103_MK918_SCD_1NMPP1-10min_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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.1x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.1x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.1x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.1x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.1x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L18_exp201105_MK679_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.1x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.1x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L18_exp201105_MK679_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L18_exp201105_MK679_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.1x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.1x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.1x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.1x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.1x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 201119L19_exp201105_MK711_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.1x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.1x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 201119L19_exp201105_MK711_SCGE_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.201119L19_exp201105_MK711_SCGE_AB101.2x36mers.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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L01_exp200917_MK919_SCD_DMSO_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L02_exp200917_MK919_SCD_CMK-01min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L03_exp200917_MK919_SCD_CMK-03min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L04_exp200917_MK919_SCD_CMK-10min_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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.1x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L10_exp2011_MK846_SCD_RAPA_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.1x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.1x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.1x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.1x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.1x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.1x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.1x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L14_exp2101_MK999_DMSO_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.1x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L18_exp2101_MK554_SCEG_DMSO_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.1x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.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 210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.210117L19_exp2101_MK554_SCEG_alpha-factor_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint