python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.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 2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.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 2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.1x36mers.sacCer3.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.2x36mers.sacCer3 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.2x36mers.sacCer3.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.1x36mers.C_glabrata_CBS138_current_chromosomes.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.2x36mers.C_glabrata_CBS138_current_chromosomes -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.2x36mers.C_glabrata_CBS138_current_chromosomes.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes