python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Cln3-MS49-SCD-rep1_S8.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 Cln3-MS49-SCD-rep1_S8.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes Cln3-MS49-SCD-rep1_S8.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Cln3-MS49-SCD-rep2_S11.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 Cln3-MS49-SCD-rep2_S11.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes Cln3-MS49-SCD-rep2_S11.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Cln3-MS49-SCE-rep1_S2.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 Cln3-MS49-SCE-rep1_S2.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes Cln3-MS49-SCE-rep1_S2.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Cln3-MS49-SCE-rep2_S5.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 Cln3-MS49-SCE-rep2_S5.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes Cln3-MS49-SCE-rep2_S5.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Whi5-MS51-SCD-rep1_S9.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 Whi5-MS51-SCD-rep1_S9.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes Whi5-MS51-SCD-rep1_S9.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Whi5-MS51-SCD-rep2_S12.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 Whi5-MS51-SCD-rep2_S12.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes Whi5-MS51-SCD-rep2_S12.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Whi5-MS51-SCE-rep1_S3.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 Whi5-MS51-SCE-rep1_S3.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes Whi5-MS51-SCE-rep1_S3.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Whi5-MS51-SCE-rep2_S6.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 Whi5-MS51-SCE-rep2_S6.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes Whi5-MS51-SCE-rep2_S6.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py WT-MS1-SCD-rep1_S7.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 WT-MS1-SCD-rep1_S7.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes WT-MS1-SCD-rep1_S7.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py WT-MS1-SCD-rep2_S10.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 WT-MS1-SCD-rep2_S10.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes WT-MS1-SCD-rep2_S10.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py WT-MS1-SCE-rep1_S1.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 WT-MS1-SCE-rep1_S1.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes WT-MS1-SCE-rep1_S1.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py WT-MS1-SCE-rep2_S4.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak 0 WT-MS1-SCE-rep2_S4.2x36mers.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes WT-MS1-SCE-rep2_S4.2x36mers.unique.nochrM.dedup.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM