python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.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 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.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 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.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 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.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 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.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 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.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