python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L391-Rosenblatt_Hannah-WT-YPGE/L391-Rosenblatt_Hannah-WT-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L391-Rosenblatt_Hannah-WT-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L392-Rosenblatt_Hannah-Asf1-YPD/L392-Rosenblatt_Hannah-Asf1-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L392-Rosenblatt_Hannah-Asf1-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L393-Goddard_Page-Asf1-YPGE/L393-Goddard_Page-Asf1-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L393-Goddard_Page-Asf1-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L394-Goddard_Page-Rtt109-YPD/L394-Goddard_Page-Rtt109-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L394-Goddard_Page-Rtt109-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L395-Wong_Wong-Rtt109-YPGE/L395-Wong_Wong-Rtt109-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L395-Wong_Wong-Rtt109-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L396-Wong_Wong-WT-YPD/L396-Wong_Wong-WT-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L396-Wong_Wong-WT-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L397-Ngo_Keri-WT-YPGE/L397-Ngo_Keri-WT-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L397-Ngo_Keri-WT-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L398-Ngo_Keri-Rtt109-YPD/L398-Ngo_Keri-Rtt109-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L398-Ngo_Keri-Rtt109-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L401-Benjamin_Alyssa-Rtt109-YPGE/L401-Benjamin_Alyssa-Rtt109-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L401-Benjamin_Alyssa-Rtt109-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L402-Benjamin_Alyssa-Asf1-YPD/L402-Benjamin_Alyssa-Asf1-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L402-Benjamin_Alyssa-Asf1-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L403-Koska_Mervenaz-WT-YPGE/L403-Koska_Mervenaz-WT-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L403-Koska_Mervenaz-WT-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L404-Koska_Mervenaz-Asf1-YPD/L404-Koska_Mervenaz-Asf1-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L404-Koska_Mervenaz-Asf1-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L405-Cotter_Daniel-Asf1-YPGE/L405-Cotter_Daniel-Asf1-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L405-Cotter_Daniel-Asf1-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L406-Cotter_Daniel-Rtt109-YPD/L406-Cotter_Daniel-Rtt109-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L406-Cotter_Daniel-Rtt109-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L407-Cheng_Jason-Rtt109-YPGE/L407-Cheng_Jason-Rtt109-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L407-Cheng_Jason-Rtt109-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L408-Cheng_Jason-WT-YPD/L408-Cheng_Jason-WT-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L408-Cheng_Jason-WT-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L409-Patel_Roshni-WT-YPGE/L409-Patel_Roshni-WT-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L409-Patel_Roshni-WT-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L410-Patel_Roshni-Asf1-YPGE/L410-Patel_Roshni-Asf1-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L410-Patel_Roshni-Asf1-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L411-Rutledge_Jarod-Asf1-YPGE/L411-Rutledge_Jarod-Asf1-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L411-Rutledge_Jarod-Asf1-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L412-Rutledge_Jarod-Rtt109-YPGE/L412-Rutledge_Jarod-Rtt109-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L412-Rutledge_Jarod-Rtt109-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L413-Tomins_Kelly-Rtt109-YPGE/L413-Tomins_Kelly-Rtt109-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L413-Tomins_Kelly-Rtt109-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L414-Tomins_Kelly-WT-YPGE/L414-Tomins_Kelly-WT-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L414-Tomins_Kelly-WT-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L415-Amador_Gabriel-WT-YPGE/L415-Amador_Gabriel-WT-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L415-Amador_Gabriel-WT-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L416-Amador_Gabriel-Rtt109-YPGE/L416-Amador_Gabriel-Rtt109-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L416-Amador_Gabriel-Rtt109-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L417-Ungar_Rachel-Asf1-YPGE/L417-Ungar_Rachel-Asf1-YPGE.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L417-Ungar_Rachel-Asf1-YPGE -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L418-Ungar_Rachel-WT-YPD/L418-Ungar_Rachel-WT-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L418-Ungar_Rachel-WT-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L419-Ma_Rosa-Rtt109-YPD/L419-Ma_Rosa-Rtt109-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L419-Ma_Rosa-Rtt109-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L420-Ma_Rosa-Asf1-YPD/L420-Ma_Rosa-Asf1-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L420-Ma_Rosa-Asf1-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L421-Maghini_Dylan-WT-YPD/L421-Maghini_Dylan-WT-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L421-Maghini_Dylan-WT-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L422-Maghini_Dylan-Asf1-YPD/L422-Maghini_Dylan-Asf1-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L422-Maghini_Dylan-Asf1-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L423-Greenwald_Emily-Asf1-YPD/L423-Greenwald_Emily-Asf1-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L423-Greenwald_Emily-Asf1-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L424-Greenwald_Emily-Rtt109-YPD/L424-Greenwald_Emily-Rtt109-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L424-Greenwald_Emily-Rtt109-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L425-Hanson_Kathryn-Rtt109-YPD/L425-Hanson_Kathryn-Rtt109-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L425-Hanson_Kathryn-Rtt109-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L426-Hanson_Kathryn-WT-YPD/L426-Hanson_Kathryn-WT-YPD.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L426-Hanson_Kathryn-WT-YPD -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L427-YPD-WT-rep1/L427-YPD-WT-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L427-YPD-WT-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L428-YPD-WT-rep2/L428-YPD-WT-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L428-YPD-WT-rep2 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L429-YPD-asf1-rep1/L429-YPD-asf1-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L429-YPD-asf1-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L430-YPD-asf1-rep2/L430-YPD-asf1-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L430-YPD-asf1-rep2 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L431-YPD-rtt109-rep1/L431-YPD-rtt109-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L431-YPD-rtt109-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L432-YPD-rtt109-rep2/L432-YPD-rtt109-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L432-YPD-rtt109-rep2 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L433-YPGE-WT-rep1/L433-YPGE-WT-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L433-YPGE-WT-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L434-YPGE-WT-rep2/L434-YPGE-WT-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L434-YPGE-WT-rep2 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L435-YPGE-asf1-rep1/L435-YPGE-asf1-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L435-YPGE-asf1-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L436-YPGE-asf1-rep2/L436-YPGE-asf1-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L436-YPGE-asf1-rep2 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L437-YPGE-rtt109-rep1/L437-YPGE-rtt109-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L437-YPGE-rtt109-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L438-YPGE-rtt109-rep2/L438-YPGE-rtt109-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L438-YPGE-rtt109-rep2 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L439-YPD-spt10-rep1/L439-YPD-spt10-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L439-YPD-spt10-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L440-YPD-spt10-rep2/L440-YPD-spt10-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L440-YPD-spt10-rep2 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L441-YPD-rlf2-rep1/L441-YPD-rlf2-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L441-YPD-rlf2-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L442-YPD-rlf2-rep2/L442-YPD-rlf2-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L442-YPD-rlf2-rep2 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L443-YPD-hir1-rep1/L443-YPD-hir1-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L443-YPD-hir1-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L444-YPD-hir1-rep2/L444-YPD-hir1-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L444-YPD-hir1-rep2 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L445-YPD-hir2-rep1/L445-YPD-hir2-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L445-YPD-hir2-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L446-YPD-hir2-rep2/L446-YPD-hir2-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L446-YPD-hir2-rep2 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L447-YPD-hir3-rep1/L447-YPD-hir3-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L447-YPD-hir3-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L448-YPD-hir3-rep2/L448-YPD-hir3-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L448-YPD-hir3-rep2 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L449-YPD-hpc2-rep1/L449-YPD-hpc2-rep1.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L449-YPD-hpc2-rep1 -RPM -uniqueBAM -singleFieldRegion &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2018-05-29-yeast-datasets/12-TIF-seq-GSE39128/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TSS-upstream500bp.bed 0 ~/ENCODE4/datasets-ATAC/L450-YPD-hpc2-rep2/L450-YPD-hpc2-rep2.2x36mers.unique.dedup.bam ~/genomes/sacCer3/sacCer3.chrom.sizes TIF-seq-updated-TSS-upstream500bp.L450-YPD-hpc2-rep2 -RPM -uniqueBAM -singleFieldRegion &