python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_00nMBE_10min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_05nMBE_10min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_00min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_05min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.1x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.2x36mers.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 2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2021-11-12-exp210929_MS63_SCGElowURA_15nMBE_10min4TU_DNA2.2x36mers.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