python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.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 2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.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 2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.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 2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.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 2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.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 2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L06_exp251120_MS8_SCD_0min-Torin.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 2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.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 2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.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 2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.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 2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.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 2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.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 2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L07_exp251120_MS8_SCD_5min-Torin.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 2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.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 2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.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 2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.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 2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.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 2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.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 2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L08_exp251120_MS8_SCD_10min-Torin.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 2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.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 2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.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 2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.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 2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.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 2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.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 2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L09_exp251120_MS8_SCD_20min-Torin.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 2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.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 2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.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 2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.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 2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.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 2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.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 2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_251123L10_exp251120_MS8_SCD_45min-Torin.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 2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.1x36mers.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 2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.2x36mers.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 2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.2x36mers.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 2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.1x36mers.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 2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.2x36mers.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 2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L12_exp251216_MS1106_SCD_10min-1NM-PP1.2x36mers.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 2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.1x36mers.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 2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.2x36mers.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 2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.2x36mers.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 2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.1x36mers.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 2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.2x36mers.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 2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L13_exp251216_MS1106_SCD_20min-1NM-PP1.2x36mers.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 2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.1x36mers.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 2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.2x36mers.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 2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.2x36mers.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 2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.1x36mers.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 2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.2x36mers.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 2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2026-02-14-LHG_260107L14_exp251216_MS1106_SCD_45min-1NM-PP1.2x36mers.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