python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py L2225-HEK293_KAS_ApexBio.2x36mers.unique.dedup.bam SAMstats-L2225-HEK293_KAS_ApexBio.2x36mers.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique.dedup.bam SAMstats-L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py L2225-HEK293_KAS_ApexBio.2x36mers.unique.bam SAMstats-L2225-HEK293_KAS_ApexBio.2x36mers.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique.bam SAMstats-L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- L2225-HEK293_KAS_ApexBio.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L2225-HEK293_KAS_ApexBio.2x36mers.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique.dedup.wig -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- L2225-HEK293_KAS_ApexBio.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L2225-HEK293_KAS_ApexBio.2x36mers.unique.dedup.5p.plus.wig -stranded + -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique.dedup.5p.plus.wig -stranded + -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- L2225-HEK293_KAS_ApexBio.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L2225-HEK293_KAS_ApexBio.2x36mers.unique.dedup.5p.minus.wig -stranded - -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique.dedup.5p.minus.wig -stranded - -notitle -uniqueBAM -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py L2225-HEK293_KAS_ApexBio.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L2225-HEK293_KAS_ApexBio.2x36mers.unique.dedup.InsLen -uniqueBAM -normalize
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L2299-HEK293_48h_dCas9_CD298_1.2x36mers.unique.dedup.InsLen -uniqueBAM -normalize