python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes