python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Camptothecin_1.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Camptothecin_1.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Camptothecin_2.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Camptothecin_2.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Camptothecin_300.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Camptothecin_300.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Camptothecin_3.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Camptothecin_3.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Camptothecin_800.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Camptothecin_800.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Clotrimazole_1.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Clotrimazole_1.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Clotrimazole_2.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Clotrimazole_2.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Clotrimazole_300.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Clotrimazole_300.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Clotrimazole_3.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Clotrimazole_3.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Clotrimazole_800.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Clotrimazole_800.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 DMSO_1-1.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.DMSO_1-1.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 DMSO_1-2.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.DMSO_1-2.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 DMSO_2-1.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.DMSO_2-1.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 DMSO_2-2.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.DMSO_2-2.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Idarubicin_1.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Idarubicin_1.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Idarubicin_2.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Idarubicin_2.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Idarubicin_300.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Idarubicin_300.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Idarubicin_3.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Idarubicin_3.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Idarubicin_800.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Idarubicin_800.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Ketoconazole_1.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Ketoconazole_1.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Ketoconazole_2.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Ketoconazole_2.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Ketoconazole_300.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Ketoconazole_300.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Ketoconazole_3.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Ketoconazole_3.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Ketoconazole_800.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Ketoconazole_800.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Miconazole_1.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Miconazole_1.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Miconazole_2.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Miconazole_2.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Miconazole_300.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Miconazole_300.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Miconazole_3.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Miconazole_3.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Miconazole_800.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Miconazole_800.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Unknown_1.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Unknown_1.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Unknown_2.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Unknown_2.counts -uniqueBAM -singleFieldRegion
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 Unknown_3.2x36mers.sacCer3.unique.nochrM.dedup.bam TSS-250bp-350bp.Unknown_3.counts -uniqueBAM -singleFieldRegion