python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL11A.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL11A.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL11B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL11B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL12B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL12B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL13A.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL13A.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL13B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL13B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL13D.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL13D.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL14B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL14B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL15A.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL15A.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL15B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL15B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL15D.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL15D.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL16A.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL16A.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL16D.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL16D.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL18A.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL18A.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL18D2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL18D2.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL19B_rep1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL19B_rep1.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL19B_rep2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL19B_rep2.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL1D_rep1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL1D_rep1.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL1D_rep2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL1D_rep2.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL2A_rep1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL2A_rep1.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL2A_rep2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL2A_rep2.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL2B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL2B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL2D.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL2D.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL3A.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL3A.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL3B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL3B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL3D.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL3D.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL4A.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL4A.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL4B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL4B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL4D.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL4D.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL5A.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL5A.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL5B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL5B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL5D.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL5D.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL6A_rep1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL6A_rep1.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL6A_rep2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL6A_rep2.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL6B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL6B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL6D.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL6D.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL7A.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL7A.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL7B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL7B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL7D.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL7D.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL8A_rep1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL8A_rep1.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL8A_rep2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL8A_rep2.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL8B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL8B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL8D1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL8D1.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL9A_rep1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL9A_rep1.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL9A_rep2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL9A_rep2.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL9B.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL9B.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SPL9D.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes SPL9D.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py Ta-input.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes Ta-input.2x36mers.InsertLength -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py Ta-input2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes Ta-input2.2x36mers.InsertLength -uniqueBAM -normalize