python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ChCUC1_halo_REP1.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes ChCUC1_halo_REP1.SE.a.plus.wig -notitle -RPM -uniqueBAM -stranded +
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ChCUC1_halo_REP1.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes ChCUC1_halo_REP1.SE.a.minus.wig -notitle -RPM -uniqueBAM -stranded -
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ChCUC1_halo_REP2.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes ChCUC1_halo_REP2.SE.a.plus.wig -notitle -RPM -uniqueBAM -stranded +
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ChCUC1_halo_REP2.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes ChCUC1_halo_REP2.SE.a.minus.wig -notitle -RPM -uniqueBAM -stranded -
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ChCUC1_halo_REP3.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes ChCUC1_halo_REP3.SE.a.plus.wig -notitle -RPM -uniqueBAM -stranded +
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ChCUC1_halo_REP3.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes ChCUC1_halo_REP3.SE.a.minus.wig -notitle -RPM -uniqueBAM -stranded -
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- halo_REP1.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes halo_REP1.SE.a.plus.wig -notitle -RPM -uniqueBAM -stranded +
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- halo_REP1.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes halo_REP1.SE.a.minus.wig -notitle -RPM -uniqueBAM -stranded -
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- halo_REP2.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes halo_REP2.SE.a.plus.wig -notitle -RPM -uniqueBAM -stranded +
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- halo_REP2.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes halo_REP2.SE.a.minus.wig -notitle -RPM -uniqueBAM -stranded -
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- halo_REP3.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes halo_REP3.SE.a.plus.wig -notitle -RPM -uniqueBAM -stranded +
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- halo_REP3.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes halo_REP3.SE.a.minus.wig -notitle -RPM -uniqueBAM -stranded -