python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L13_exp210422_MS207_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L13_exp210422_MS207_SCD_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 2021-05-25-21508L13_exp210422_MS207_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L13_exp210422_MS207_SCD_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 2021-05-25-21508L13_exp210422_MS207_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L13_exp210422_MS207_SCD_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 2021-05-25-21508L13_exp210422_MS207_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L13_exp210422_MS207_SCD_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L13_exp210422_MS207_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L13_exp210422_MS207_SCD_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L13_exp210422_MS207_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L13_exp210422_MS207_SCD_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.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 2021-05-25-21508L14_exp210422_MS208_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L14_exp210422_MS208_SCD_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 2021-05-25-21508L14_exp210422_MS208_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L14_exp210422_MS208_SCD_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 2021-05-25-21508L14_exp210422_MS208_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L14_exp210422_MS208_SCD_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 2021-05-25-21508L14_exp210422_MS208_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L14_exp210422_MS208_SCD_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L14_exp210422_MS208_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L14_exp210422_MS208_SCD_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L14_exp210422_MS208_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L14_exp210422_MS208_SCD_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.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 2021-05-25-21508L15_exp210422_MS299_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L15_exp210422_MS299_SCD_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 2021-05-25-21508L15_exp210422_MS299_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L15_exp210422_MS299_SCD_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 2021-05-25-21508L15_exp210422_MS299_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L15_exp210422_MS299_SCD_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 2021-05-25-21508L15_exp210422_MS299_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L15_exp210422_MS299_SCD_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L15_exp210422_MS299_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L15_exp210422_MS299_SCD_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L15_exp210422_MS299_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L15_exp210422_MS299_SCD_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.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 2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_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 2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_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 2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_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 2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L16_exp210422_MS207_SCD_RAPA-40min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.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 2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_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 2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_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 2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_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 2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L17_exp210422_MS208_SCD_RAPA-40min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.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 2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_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 2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_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 2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_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 2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L18_exp210422_MS299_SCD_RAPA-40min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.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 2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_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 2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_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 2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_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 2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L19_exp210422_MS207_SCD_RAPA-60min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.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 2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_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 2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_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 2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_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 2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L20_exp210422_MS208_SCD_RAPA-60min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.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 2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_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 2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_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 2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_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 2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L21_exp210422_MS299_SCD_RAPA-60min_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.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 2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_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 2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_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 2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_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 2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L22_exp210422_MS207_SCD_RAPA-24hr_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.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 2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_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 2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_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 2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_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 2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L23_exp210422_MS208_SCD_RAPA-24hr_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.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 2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_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 2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_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 2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_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 2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_DNA.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-05-25-21508L24_exp210422_MS299_SCD_RAPA-24hr_DNA.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes