python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-CXCR4-0hr-A9.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-CXCR4-0hr-A9.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-CXCR4-0hr-A9.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-CXCR4-0hr-B9.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-CXCR4-0hr-B9.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-CXCR4-0hr-B9.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-CXCR4-48hr-C9.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-CXCR4-48hr-C9.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-CXCR4-48hr-C9.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-CXCR4-48hr-D9.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-CXCR4-48hr-D9.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-CXCR4-48hr-D9.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-CXCR5-0hr-A10.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-CXCR5-0hr-A10.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-CXCR5-0hr-A10.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-CXCR5-0hr-B10.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-CXCR5-0hr-B10.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-CXCR5-0hr-B10.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-CXCR5-48hr-C10.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-CXCR5-48hr-C10.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-CXCR5-48hr-C10.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-CXCR5-48hr-D10.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-CXCR5-48hr-D10.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-CXCR5-48hr-D10.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-FOXA1-0hr-A7.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-FOXA1-0hr-A7.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-FOXA1-0hr-A7.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-FOXA1-0hr-B7.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-FOXA1-0hr-B7.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-FOXA1-0hr-B7.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-FOXA1-48hr-C7.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-FOXA1-48hr-C7.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-FOXA1-48hr-C7.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-FOXA1-48hr-D7.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-FOXA1-48hr-D7.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-FOXA1-48hr-D7.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA1-0hr-A1.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA1-0hr-A1.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA1-0hr-A1.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA1-0hr-B1.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA1-0hr-B1.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA1-0hr-B1.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA1-48hr-C1.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA1-48hr-C1.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA1-48hr-C1.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA1-48hr-D1.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA1-48hr-D1.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA1-48hr-D1.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA2-0hr-A2.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA2-0hr-A2.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA2-0hr-A2.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA2-0hr-B2.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA2-0hr-B2.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA2-0hr-B2.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA2-48hr-C2.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA2-48hr-C2.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA2-48hr-C2.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA2-48hr-D2.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA2-48hr-D2.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA2-48hr-D2.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA3-0hr-A3.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA3-0hr-A3.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA3-0hr-A3.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA3-0hr-B3.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA3-0hr-B3.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA3-0hr-B3.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA3-48hr-C3.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA3-48hr-C3.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA3-48hr-C3.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA3-48hr-D3.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA3-48hr-D3.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA3-48hr-D3.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA6-0hr-A4.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA6-0hr-A4.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA6-0hr-A4.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA6-0hr-B4.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA6-0hr-B4.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA6-0hr-B4.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA6-48hr-C4.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA6-48hr-C4.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA6-48hr-C4.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-GATA6-48hr-D4.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-GATA6-48hr-D4.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-GATA6-48hr-D4.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-MyoD-0hr-A5.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-MyoD-0hr-A5.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-MyoD-0hr-A5.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-MyoD-0hr-B5.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-MyoD-0hr-B5.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-MyoD-0hr-B5.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-MyoD-48hr-C5.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-MyoD-48hr-C5.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-MyoD-48hr-C5.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-MyoD-48hr-D5.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-MyoD-48hr-D5.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-MyoD-48hr-D5.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-no_guide-0hr-A12.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-no_guide-0hr-A12.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-no_guide-0hr-A12.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-no_guide-0hr-B12.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-no_guide-0hr-B12.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-no_guide-0hr-B12.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-no_guide-48hr-C12.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-no_guide-48hr-C12.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-no_guide-48hr-C12.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-no_guide-48hr-D12.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-no_guide-48hr-D12.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-no_guide-48hr-D12.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-scramble-0hr-A11.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-scramble-0hr-A11.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-scramble-0hr-A11.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-scramble-0hr-B11.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-scramble-0hr-B11.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-scramble-0hr-B11.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-scramble-48hr-C11.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-scramble-48hr-C11.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-scramble-48hr-C11.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-scramble-48hr-D11.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-scramble-48hr-D11.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-scramble-48hr-D11.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-SIX1-0hr-A6.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-SIX1-0hr-A6.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-SIX1-0hr-A6.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-SIX1-0hr-B6.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-SIX1-0hr-B6.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-SIX1-0hr-B6.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-SIX1-48hr-C6.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-SIX1-48hr-C6.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-SIX1-48hr-C6.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-SIX1-48hr-D6.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-SIX1-48hr-D6.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-SIX1-48hr-D6.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-SOX2-0hr-A8.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-SOX2-0hr-A8.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-SOX2-0hr-A8.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-SOX2-0hr-B8.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-SOX2-0hr-B8.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-SOX2-0hr-B8.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-SOX2-48hr-C8.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-SOX2-48hr-C8.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-SOX2-48hr-C8.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 2019-06-13-SOX2-48hr-D8.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.gz 0 2019-06-13-SOX2-48hr-D8.2x36mers.hg38-female.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  2019-06-13-SOX2-48hr-D8.2x36mers.hg38-female.unique.nochrM.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM