python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L209-S2_Ecd_0h_Rep1/L209-S2_Ecd_0h_Rep1.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L209-S2_Ecd_0h_Rep1.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L210-S2_Ecd_0h_Rep2/L210-S2_Ecd_0h_Rep2.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L210-S2_Ecd_0h_Rep2.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L211-S2_Ecd_2h_Rep1/L211-S2_Ecd_2h_Rep1.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L211-S2_Ecd_2h_Rep1.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L212-S2_Ecd_2h_Rep2/L212-S2_Ecd_2h_Rep2.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L212-S2_Ecd_2h_Rep2.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L213-S2_Ecd_4h_Rep1/L213-S2_Ecd_4h_Rep1.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L213-S2_Ecd_4h_Rep1.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L214-S2_Ecd_4h_Rep2/L214-S2_Ecd_4h_Rep2.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L214-S2_Ecd_4h_Rep2.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L215-S2_Ecd_8h_Rep1/L215-S2_Ecd_8h_Rep1.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L215-S2_Ecd_8h_Rep1.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L216-S2_Ecd_8h_Rep2/L216-S2_Ecd_8h_Rep2.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L216-S2_Ecd_8h_Rep2.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L217-S2_Ecd_12h_Rep1/L217-S2_Ecd_12h_Rep1.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L217-S2_Ecd_12h_Rep1.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L218-S2_Ecd_12h_Rep2/L218-S2_Ecd_12h_Rep2.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L218-S2_Ecd_12h_Rep2.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L219-S2_Ecd_24h_Rep1/L219-S2_Ecd_24h_Rep1.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L219-S2_Ecd_24h_Rep1.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L220-S2_Ecd_24h_Rep2/L220-S2_Ecd_24h_Rep2.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L220-S2_Ecd_24h_Rep2.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L221-S2_no_Ecd_24h_Rep1/L221-S2_no_Ecd_24h_Rep1.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L221-S2_no_Ecd_24h_Rep1.RPM -RPM -uniqueBAM -singleFieldRegion
python ~/code/bedRPKMfromBAM.py IDR-0.10.200bp.100bp-radius.bed 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L222-S2_no_Ecd_24h_Rep2/L222-S2_no_Ecd_24h_Rep2.2x36mers.dm6.unique.dedup.nochrM.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes IDR-0.10.200bp.100bp-radius.L222-S2_no_Ecd_24h_Rep2.RPM -RPM -uniqueBAM -singleFieldRegion