python ~/code/bedRPKMfromBAM.py	L5770-HEK_SPI1_1_SPI_ChIP.2x36mers.unique.dedup.MACS-2.1.0_peaks.narrowPeak.gz 0	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5770-HEK_SPI1_1_SPI_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5771-HEK_SPI1_0.5_SPI_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5772-HEK_SPI1_0.25_SPI_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5773-HEK_SPI1_0.05_SPI_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5774-HEK_SOX2_1_SOX_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5775-HEK_SOX2_0.75_SOX_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5776-HEK_SOX2_0.5_SOX_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5777-HEK_SOX2_0.25_SOX_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5778-HEK_SOX2_0.05_SOX_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5779-HEK_IRF4_1_IRF4_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5780-HEK_IRF4_0.5_IRF4_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5781-HEK_IRF4_0.25_IRF4_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5782-HEK_IRF4_0.05_IRF4_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5783-HEK_LEF1_1_LEF1_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5784-HEK_LEF1_0.5_LEF1_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5785-HEK_LEF1_0.25_LEF1_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5786-HEK_LEF1_0.05_LEF1_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5787-HEK_ALX4_1_ALX4-FLAG_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5788-HEK_ALX4_0.5_ALX4-FLAG_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5789-HEK_ALX4_0.25_ALX4-FLAG_ChIP/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	/oak/stanford/groups/wjg/marinovg/ENCODE4/datasets-ChIP/L5790-HEK_ALX4_0.05_ALX4-FLAG_ChIP/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 &