python ~/code/bedRPKMfromBAM.py L5770-HEK_SPI1_1_SPI_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5770-HEK_SPI1_1_SPI_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5770-HEK_SPI1_1_SPI_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5771-HEK_SPI1_0.5_SPI_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5771-HEK_SPI1_0.5_SPI_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5771-HEK_SPI1_0.5_SPI_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5772-HEK_SPI1_0.25_SPI_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5772-HEK_SPI1_0.25_SPI_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5772-HEK_SPI1_0.25_SPI_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5773-HEK_SPI1_0.05_SPI_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5773-HEK_SPI1_0.05_SPI_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5773-HEK_SPI1_0.05_SPI_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5774-HEK_SOX2_1_SOX_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5774-HEK_SOX2_1_SOX_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5774-HEK_SOX2_1_SOX_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5775-HEK_SOX2_0.75_SOX_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5775-HEK_SOX2_0.75_SOX_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5775-HEK_SOX2_0.75_SOX_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5776-HEK_SOX2_0.5_SOX_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5776-HEK_SOX2_0.5_SOX_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5776-HEK_SOX2_0.5_SOX_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5777-HEK_SOX2_0.25_SOX_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5777-HEK_SOX2_0.25_SOX_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5777-HEK_SOX2_0.25_SOX_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5778-HEK_SOX2_0.05_SOX_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5778-HEK_SOX2_0.05_SOX_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5778-HEK_SOX2_0.05_SOX_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5779-HEK_IRF4_1_IRF4_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5779-HEK_IRF4_1_IRF4_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5779-HEK_IRF4_1_IRF4_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5780-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5780-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5780-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5781-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5781-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5781-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5782-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5782-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5782-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5783-HEK_LEF1_1_LEF1_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5783-HEK_LEF1_1_LEF1_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5783-HEK_LEF1_1_LEF1_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5784-HEK_LEF1_0.5_LEF1_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5784-HEK_LEF1_0.5_LEF1_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5784-HEK_LEF1_0.5_LEF1_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5785-HEK_LEF1_0.25_LEF1_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5785-HEK_LEF1_0.25_LEF1_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5785-HEK_LEF1_0.25_LEF1_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5786-HEK_LEF1_0.05_LEF1_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5786-HEK_LEF1_0.05_LEF1_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5786-HEK_LEF1_0.05_LEF1_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5787-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5787-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5787-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5788-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5788-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5788-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5789-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5789-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5789-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python ~/code/bedRPKMfromBAM.py L5790-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0 L5790-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5790-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &