python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ABI19_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ABI19_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ABI19_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ABI19_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ABI34_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ABI34_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ABI34_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ABI34_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ABI8_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ABI8_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ABI8_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ABI8_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF10_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF10_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF13_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF13_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF14_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF14_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF16_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF16_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF18_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF18_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF25_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF25_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF27_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF27_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF29_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF29_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF34_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF34_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF35_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF35_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF36_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF36_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF39_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF39_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF4_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF4_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARF7_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARF7_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARR5_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARR5_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ARR5_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ARR5_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BAF1_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BAF1_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BAF1_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BAF1_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BAFL12_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BAFL12_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BAFL3_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BAFL3_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH106_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH106_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH106_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH106_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH113_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH113_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH113_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH113_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH125_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH125_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH135_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH135_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH135_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH135_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH149_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH149_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH149_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH149_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH14_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH14_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH150_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH150_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH150_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH150_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH168_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH168_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH168_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH168_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH17_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH17_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH17_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH17_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH52_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH52_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH52_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH52_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH57_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH57_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH57_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH57_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH61_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH61_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH61_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH61_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH67_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH67_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH67_BA1_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH67_BA1_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH85_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH85_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH85_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH85_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH91_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH91_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH91_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH91_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH99_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH99_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BHLH99_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH99_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP105_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP105_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP105_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP105_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP106_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP106_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP106_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP106_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP111_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP111_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP111_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP111_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP112_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP112_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP112_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP112_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP115_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP115_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP115_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP115_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP124_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP124_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP124_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP124_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP128_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP128_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP128_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP128_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP12_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP12_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP12_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP12_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP13_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP13_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP13_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP13_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP160_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP160_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP160_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP160_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP1_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP1_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP1_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP1_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP21_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP21_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP21_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP21_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP23_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP23_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP23_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP23_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP25_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP25_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP25_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP25_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP27_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP27_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP27_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP27_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP2_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP2_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP2_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP2_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP34_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP34_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP34_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP34_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP39_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP39_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP39_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP39_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP40_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP40_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP40_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP40_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP41_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP41_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP41_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP41_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP48_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP48_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP48_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP48_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP52_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP52_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP52_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP52_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP54_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP54_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP54_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP54_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP57_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP57_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP58_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP58_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP58_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP58_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP61_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP61_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP61_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP61_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP62_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP62_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP62_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP62_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP68_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP68_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP68_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP68_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP70_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP70_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP70_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP70_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP72_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP72_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP79_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP79_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP79_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP79_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP84_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP84_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP84_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP84_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP86_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP86_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP86_rep1_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP86_rep1_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP86_rep2_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP86_rep2_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP87_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP87_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP87_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP87_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP90_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP90_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP90_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP90_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP91_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP91_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP91_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP91_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP92_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP92_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP92_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP92_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP94_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP94_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP94_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP94_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP96_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP96_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP99_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP99_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZIP99_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP99_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZR1_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZR1_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BZR1_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZR1_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py CA2P13_CA3P1_CA5P7_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes CA2P13_CA3P1_CA5P7_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py CA2P13_CA3P1_CA5P7_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes CA2P13_CA3P1_CA5P7_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py CA2P13_CA3P4_CA5P7_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes CA2P13_CA3P4_CA5P7_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py CA2P13_CA3P4_CA5P7_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes CA2P13_CA3P4_CA5P7_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py CCHH2_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes CCHH2_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py CCHH2_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes CCHH2_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH113_BHLH125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH113_BHLH125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH113_BHLH168_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH113_BHLH168_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH135_BHLH125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH135_BHLH125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH135_BHLH168_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH135_BHLH168_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH14_BHLH125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH14_BHLH125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH14_BHLH168_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH14_BHLH168_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH150_BHLH125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH150_BHLH125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH150_BHLH168_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH150_BHLH168_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH52_BHLH125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH52_BHLH125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH52_BHLH168_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH52_BHLH168_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH61_BHLH125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH61_BHLH125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH61_BHLH168_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH61_BHLH168_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH67_BHLH125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH67_BHLH125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH67_BHLH168_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH67_BHLH168_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH85_BHLH125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH85_BHLH125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH85_BHLH125_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH85_BHLH125_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH85_BHLH168_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH85_BHLH168_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH92_BHLH125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH92_BHLH125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DD_BHLH92_BHLH168_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DD_BHLH92_BHLH168_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DOF1_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DOF1_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DOF1_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DOF1_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DOF24_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DOF24_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py DOF24_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DOF24_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB126_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB126_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB126_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB126_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB138_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB138_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB145_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB145_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB145_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB145_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB149_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB149_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB149_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB149_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB183_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB183_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB183_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB183_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB201_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB201_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB201_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB201_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB24_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB24_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB29_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB29_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB2_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB2_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB2_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB2_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB36_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB36_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB36_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB36_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB46_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB46_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB46_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB46_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB49_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB49_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB49_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB49_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB4_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB4_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB4_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB4_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB53_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB53_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB53_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB53_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB87_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB87_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py EREB87_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB87_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GATA20_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GATA20_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GATA20_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GATA20_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GBP10_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GBP10_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GBP10_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GBP10_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GBP11_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GBP11_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GBP11_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GBP11_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GBP4_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GBP4_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GBP4_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GBP4_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK17_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK17_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK17_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK17_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK20_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK20_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK20_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK20_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK21_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK21_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK21_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK21_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK44_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK44_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK44_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK44_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK47_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK47_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK47_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK47_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK48_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK48_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK48_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK48_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK53_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK53_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK53_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK53_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK56_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK56_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GLK56_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GLK56_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GRF2_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GRF2_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GRF2_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GRF2_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GRF3_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GRF3_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GRF3_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GRF3_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GRF6_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GRF6_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GRF6_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GRF6_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GRF7_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GRF7_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GRF7_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GRF7_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GRF9_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GRF9_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py GRF9_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes GRF9_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HALO-GST_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HALO-GST_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB102_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB102_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB102_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB102_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB117_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB117_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB117_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB117_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB122_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB122_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB122_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB122_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB15_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB15_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB15_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB15_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB22_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB22_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB22_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB22_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB54_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB54_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB54_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB54_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB67_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB67_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB67_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB67_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB68_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB68_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HB68_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB68_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HSF10_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HSF10_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HSF10_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HSF10_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HSF24_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HSF24_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HSF24_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HSF24_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HSF25_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HSF25_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HSF25_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HSF25_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HSF7_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HSF7_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py HSF7_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HSF7_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LBD16_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes LBD16_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LBD19_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes LBD19_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LBD37_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes LBD37_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LBD37_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes LBD37_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py LBD5_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes LBD5_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS12_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS12_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS12_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS12_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS43_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS43_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS43_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS43_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS68_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS68_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS68_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS68_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS69_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS69_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS69_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS69_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS72_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS72_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS72_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS72_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS73_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS73_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MADS73_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MADS73_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB131_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB131_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB131_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB131_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB138_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB138_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB138_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB138_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB40_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB40_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB40_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB40_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB50_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB50_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB50_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB50_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB73_DED1_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB73_DED1_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB83_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB83_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB83_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB83_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYB94_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB94_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYBR101_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR101_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYBR101_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR101_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYBR111_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR111_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYBR111_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR111_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYBR17_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR17_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYBR17_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR17_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYBR52_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR52_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYBR52_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR52_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYBR58_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR58_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py MYBR58_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR58_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC115_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC115_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC115_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC115_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC116_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC116_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC116_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC116_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC12_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC12_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC12_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC12_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC20_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC20_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC20_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC20_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC25_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC25_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC25_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC25_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC27_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC27_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC27_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC27_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC28_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC28_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC28_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC28_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC33_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC33_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC33_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC33_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC3_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC3_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC3_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC3_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC42_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC42_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC42_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC42_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC49_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC49_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC49_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC49_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC71_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC71_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC71_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC71_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC74_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC74_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC74_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC74_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC86_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC86_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC86_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC86_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NAC91_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NAC91_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NFYA1_LEC1_CA5P16_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NFYA1_LEC1_CA5P16_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NFYA1_LEC1_CA5P16_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NFYA1_LEC1_CA5P16_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NKD1_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NKD1_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NKD1_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NKD1_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NKD2_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NKD2_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NKD2_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NKD2_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NLP14_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NLP14_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py NLP14_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NLP14_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP15_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP15_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP15_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP15_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP1_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP1_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP1_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP1_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP2_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP2_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP2_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP2_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP30_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP30_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP30_rep1_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP30_rep1_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP30_rep2_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP30_rep2_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP32_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP32_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP32_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP32_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP6_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP6_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SBP8_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes SBP8_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP11_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP11_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP11_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP11_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP15_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP15_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP15_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP15_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP2_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP2_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP2_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP2_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP30_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP30_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP30_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP30_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP3_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP3_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP4_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP4_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP4_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP4_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP5_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP5_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP5_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP5_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP8_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP8_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py TCP8_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TCP8_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py THX16_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes THX16_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py THX16_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes THX16_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py THX20_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes THX20_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py THX20_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes THX20_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py THX26_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes THX26_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py THX26_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes THX26_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY11_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY11_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY11_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY11_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY125_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY125_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY125_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY125_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY53_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY53_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY53_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY53_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY57_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY57_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY57_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY57_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY64_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY64_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY64_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY64_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY82_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY82_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py WRKY82_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY82_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py YAB2_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes YAB2_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py YAB2_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes YAB2_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZHD15_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZHD15_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZHD15_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZHD15_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZHD1_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZHD1_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZHD1_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZHD1_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZHD21_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZHD21_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZHD21_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZHD21_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZHD4_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZHD4_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZHD4_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZHD4_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZHD5_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZHD5_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZHD5_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZHD5_Mo17.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZIM2_B73.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZIM2_B73.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ZIM2_Mo17.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZIM2_Mo17.2x36mers.InsertLength -uniqueBAM -normalize