python ~/code/bedRPKMfromBAM.py SPL11A.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 140354543
python ~/code/bedRPKMfromBAM.py SPL11B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 103639440
python ~/code/bedRPKMfromBAM.py SPL12B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 261512484
python ~/code/bedRPKMfromBAM.py SPL13A.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 133289314
python ~/code/bedRPKMfromBAM.py SPL13B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 102159123
python ~/code/bedRPKMfromBAM.py SPL13D.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 49970103
python ~/code/bedRPKMfromBAM.py SPL14B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 114223693
python ~/code/bedRPKMfromBAM.py SPL15A.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 148445901
python ~/code/bedRPKMfromBAM.py SPL15B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 73243311
python ~/code/bedRPKMfromBAM.py SPL15D.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 180802981
python ~/code/bedRPKMfromBAM.py SPL16A.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 109869218
python ~/code/bedRPKMfromBAM.py SPL16D.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 84555595
python ~/code/bedRPKMfromBAM.py SPL18A.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 138189176
python ~/code/bedRPKMfromBAM.py SPL18D2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 122535948
python ~/code/bedRPKMfromBAM.py SPL19B_rep1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 31608868
python ~/code/bedRPKMfromBAM.py SPL19B_rep2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 47390393
python ~/code/bedRPKMfromBAM.py SPL1D_rep1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 32667032
python ~/code/bedRPKMfromBAM.py SPL1D_rep2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 124159677
python ~/code/bedRPKMfromBAM.py SPL2A_rep1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 88714568
python ~/code/bedRPKMfromBAM.py SPL2A_rep2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 20158581
python ~/code/bedRPKMfromBAM.py SPL2B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 34870560
python ~/code/bedRPKMfromBAM.py SPL2D.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 115427494
python ~/code/bedRPKMfromBAM.py SPL3A.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 76287867
python ~/code/bedRPKMfromBAM.py SPL3B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 134971104
python ~/code/bedRPKMfromBAM.py SPL3D.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 61482312
python ~/code/bedRPKMfromBAM.py SPL4A.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 49924994
python ~/code/bedRPKMfromBAM.py SPL4B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 152132726
python ~/code/bedRPKMfromBAM.py SPL4D.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 62518045
python ~/code/bedRPKMfromBAM.py SPL5A.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 25267699
python ~/code/bedRPKMfromBAM.py SPL5B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 92310009
python ~/code/bedRPKMfromBAM.py SPL5D.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 79509119
python ~/code/bedRPKMfromBAM.py SPL6A_rep1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 33195354
python ~/code/bedRPKMfromBAM.py SPL6A_rep2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 36105276
python ~/code/bedRPKMfromBAM.py SPL6B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 95727728
python ~/code/bedRPKMfromBAM.py SPL6D.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 63426571
python ~/code/bedRPKMfromBAM.py SPL7A.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 82798084
python ~/code/bedRPKMfromBAM.py SPL7B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 35204427
python ~/code/bedRPKMfromBAM.py SPL7D.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 107582619
python ~/code/bedRPKMfromBAM.py SPL8A_rep1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 114395295
python ~/code/bedRPKMfromBAM.py SPL8A_rep2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 27263204
python ~/code/bedRPKMfromBAM.py SPL8B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 311558739
python ~/code/bedRPKMfromBAM.py SPL8D1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 74679971
python ~/code/bedRPKMfromBAM.py SPL9A_rep1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 21872455
python ~/code/bedRPKMfromBAM.py SPL9A_rep2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 109431665
python ~/code/bedRPKMfromBAM.py SPL9B.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 156632282
python ~/code/bedRPKMfromBAM.py SPL9D.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 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.PE.a.MACS-2.1.0_peaks.RPM -RPM -totalReadNumber 72024065