python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-07-13-210603L01_exp210531_MS207_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L01_exp210531_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 2021-07-13-210603L01_exp210531_MS207_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L01_exp210531_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 2021-07-13-210603L01_exp210531_MS207_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L01_exp210531_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 2021-07-13-210603L01_exp210531_MS207_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L01_exp210531_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 2021-07-13-210603L01_exp210531_MS207_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L01_exp210531_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 2021-07-13-210603L01_exp210531_MS207_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L01_exp210531_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 2021-07-13-210603L02_exp210531_MS208_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L02_exp210531_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 2021-07-13-210603L02_exp210531_MS208_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L02_exp210531_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 2021-07-13-210603L02_exp210531_MS208_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L02_exp210531_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 2021-07-13-210603L02_exp210531_MS208_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L02_exp210531_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 2021-07-13-210603L02_exp210531_MS208_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L02_exp210531_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 2021-07-13-210603L02_exp210531_MS208_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L02_exp210531_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 2021-07-13-210603L03_exp210531_MS294_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L03_exp210531_MS294_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 2021-07-13-210603L03_exp210531_MS294_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L03_exp210531_MS294_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 2021-07-13-210603L03_exp210531_MS294_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L03_exp210531_MS294_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 2021-07-13-210603L03_exp210531_MS294_SCD_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L03_exp210531_MS294_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 2021-07-13-210603L03_exp210531_MS294_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L03_exp210531_MS294_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 2021-07-13-210603L03_exp210531_MS294_SCD_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L03_exp210531_MS294_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 2021-07-13-210603L04_exp210531_MS207_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L04_exp210531_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 2021-07-13-210603L04_exp210531_MS207_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L04_exp210531_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 2021-07-13-210603L04_exp210531_MS207_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L04_exp210531_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 2021-07-13-210603L04_exp210531_MS207_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L04_exp210531_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 2021-07-13-210603L04_exp210531_MS207_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L04_exp210531_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 2021-07-13-210603L04_exp210531_MS207_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L04_exp210531_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 2021-07-13-210603L05_exp210531_MS208_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L05_exp210531_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 2021-07-13-210603L05_exp210531_MS208_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L05_exp210531_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 2021-07-13-210603L05_exp210531_MS208_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L05_exp210531_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 2021-07-13-210603L05_exp210531_MS208_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L05_exp210531_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 2021-07-13-210603L05_exp210531_MS208_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L05_exp210531_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 2021-07-13-210603L05_exp210531_MS208_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L05_exp210531_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 2021-07-13-210603L06_exp210531_MS294_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L06_exp210531_MS294_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 2021-07-13-210603L06_exp210531_MS294_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L06_exp210531_MS294_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 2021-07-13-210603L06_exp210531_MS294_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L06_exp210531_MS294_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 2021-07-13-210603L06_exp210531_MS294_SCD_RAPA-40min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L06_exp210531_MS294_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 2021-07-13-210603L06_exp210531_MS294_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L06_exp210531_MS294_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 2021-07-13-210603L06_exp210531_MS294_SCD_RAPA-40min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L06_exp210531_MS294_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 2021-07-13-210603L07_exp210531_MS207_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L07_exp210531_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 2021-07-13-210603L07_exp210531_MS207_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L07_exp210531_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 2021-07-13-210603L07_exp210531_MS207_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L07_exp210531_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 2021-07-13-210603L07_exp210531_MS207_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L07_exp210531_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 2021-07-13-210603L07_exp210531_MS207_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L07_exp210531_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 2021-07-13-210603L07_exp210531_MS207_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L07_exp210531_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 2021-07-13-210603L08_exp210531_MS208_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L08_exp210531_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 2021-07-13-210603L08_exp210531_MS208_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L08_exp210531_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 2021-07-13-210603L08_exp210531_MS208_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L08_exp210531_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 2021-07-13-210603L08_exp210531_MS208_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L08_exp210531_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 2021-07-13-210603L08_exp210531_MS208_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L08_exp210531_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 2021-07-13-210603L08_exp210531_MS208_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L08_exp210531_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 2021-07-13-210603L09_exp210531_MS294_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L09_exp210531_MS294_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 2021-07-13-210603L09_exp210531_MS294_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L09_exp210531_MS294_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 2021-07-13-210603L09_exp210531_MS294_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L09_exp210531_MS294_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 2021-07-13-210603L09_exp210531_MS294_SCD_RAPA-60min_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L09_exp210531_MS294_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 2021-07-13-210603L09_exp210531_MS294_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L09_exp210531_MS294_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 2021-07-13-210603L09_exp210531_MS294_SCD_RAPA-60min_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L09_exp210531_MS294_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 2021-07-13-210603L10_exp210531_MS207_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L10_exp210531_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 2021-07-13-210603L10_exp210531_MS207_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L10_exp210531_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 2021-07-13-210603L10_exp210531_MS207_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L10_exp210531_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 2021-07-13-210603L10_exp210531_MS207_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L10_exp210531_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 2021-07-13-210603L10_exp210531_MS207_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L10_exp210531_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 2021-07-13-210603L10_exp210531_MS207_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L10_exp210531_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 2021-07-13-210603L11_exp210531_MS208_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L11_exp210531_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 2021-07-13-210603L11_exp210531_MS208_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L11_exp210531_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 2021-07-13-210603L11_exp210531_MS208_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L11_exp210531_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 2021-07-13-210603L11_exp210531_MS208_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L11_exp210531_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 2021-07-13-210603L11_exp210531_MS208_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L11_exp210531_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 2021-07-13-210603L11_exp210531_MS208_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L11_exp210531_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 2021-07-13-210603L12_exp210531_MS294_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L12_exp210531_MS294_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 2021-07-13-210603L12_exp210531_MS294_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L12_exp210531_MS294_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 2021-07-13-210603L12_exp210531_MS294_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L12_exp210531_MS294_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 2021-07-13-210603L12_exp210531_MS294_SCD_RAPA-24hr_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L12_exp210531_MS294_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 2021-07-13-210603L12_exp210531_MS294_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L12_exp210531_MS294_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 2021-07-13-210603L12_exp210531_MS294_SCD_RAPA-24hr_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L12_exp210531_MS294_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 2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.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 2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.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 2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.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 2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.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 2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.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 2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L13_exp210422_MS207_SCD_DNA-B.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 2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.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 2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.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 2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.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 2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.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 2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.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 2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L14_exp210422_MS208_SCD_DNA-B.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 2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.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 2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.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 2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.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 2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.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 2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.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 2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L15_exp210422_MS295_SCD_DNA-B.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 2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L16_exp210422_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L17_exp210422_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L18_exp210422_MS295_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L19_exp210422_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L20_exp210422_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L21_exp210422_MS295_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L22_exp210422_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L23_exp210422_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L24_exp210422_MS295_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.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 2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.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 2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.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 2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.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 2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.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 2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L25_exp210531_MS207_SCD_DNA-B.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 2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.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 2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.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 2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.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 2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.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 2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.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 2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L26_exp210531_MS208_SCD_DNA-B.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 2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.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 2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.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 2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.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 2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.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 2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.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 2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L27_exp210531_MS294_SCD_DNA-B.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 2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L28_exp210531_MS207_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L29_exp210531_MS208_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L30_exp210531_MS294_SCD_RAPA-40min_DNA-B.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 2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L31_exp210531_MS207_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L32_exp210531_MS208_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L33_exp210531_MS294_SCD_RAPA-60min_DNA-B.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 2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L34_exp210531_MS207_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L35_exp210531_MS208_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.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 2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-07-13-210603L36_exp210531_MS294_SCD_RAPA-24hr_DNA-B.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