python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B001_180525L01_exp180222_MS01_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B001_180525L01_exp180222_MS01_SCGE_input.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 B001_180525L01_exp180222_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B001_180525L01_exp180222_MS01_SCGE_input.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 B001_180525L01_exp180222_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B001_180525L01_exp180222_MS01_SCGE_input.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 B001_180525L01_exp180222_MS01_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B001_180525L01_exp180222_MS01_SCGE_input.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 B001_180525L01_exp180222_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B001_180525L01_exp180222_MS01_SCGE_input.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 B001_180525L01_exp180222_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B001_180525L01_exp180222_MS01_SCGE_input.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 B007_180525L04_exp180222_MS01_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B007_180525L04_exp180222_MS01_SCGE_AB01.1x36mers.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 B007_180525L04_exp180222_MS01_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B007_180525L04_exp180222_MS01_SCGE_AB01.2x36mers.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 B007_180525L04_exp180222_MS01_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B007_180525L04_exp180222_MS01_SCGE_AB01.2x36mers.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 B007_180525L04_exp180222_MS01_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B007_180525L04_exp180222_MS01_SCGE_AB01.1x36mers.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 B007_180525L04_exp180222_MS01_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B007_180525L04_exp180222_MS01_SCGE_AB01.2x36mers.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 B007_180525L04_exp180222_MS01_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B007_180525L04_exp180222_MS01_SCGE_AB01.2x36mers.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 B013_180525L07_exp180222_MS01_SCGE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B013_180525L07_exp180222_MS01_SCGE_AB02.1x36mers.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 B013_180525L07_exp180222_MS01_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B013_180525L07_exp180222_MS01_SCGE_AB02.2x36mers.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 B013_180525L07_exp180222_MS01_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B013_180525L07_exp180222_MS01_SCGE_AB02.2x36mers.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 B013_180525L07_exp180222_MS01_SCGE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B013_180525L07_exp180222_MS01_SCGE_AB02.1x36mers.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 B013_180525L07_exp180222_MS01_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B013_180525L07_exp180222_MS01_SCGE_AB02.2x36mers.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 B013_180525L07_exp180222_MS01_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B013_180525L07_exp180222_MS01_SCGE_AB02.2x36mers.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 B019_180525L10_exp180222_MS01_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B019_180525L10_exp180222_MS01_SCGE_AB05.1x36mers.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 B019_180525L10_exp180222_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B019_180525L10_exp180222_MS01_SCGE_AB05.2x36mers.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 B019_180525L10_exp180222_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B019_180525L10_exp180222_MS01_SCGE_AB05.2x36mers.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 B019_180525L10_exp180222_MS01_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B019_180525L10_exp180222_MS01_SCGE_AB05.1x36mers.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 B019_180525L10_exp180222_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B019_180525L10_exp180222_MS01_SCGE_AB05.2x36mers.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 B019_180525L10_exp180222_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B019_180525L10_exp180222_MS01_SCGE_AB05.2x36mers.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 B025_180525L13_exp180222_MS01_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B025_180525L13_exp180222_MS01_SCGE_AB20.1x36mers.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 B025_180525L13_exp180222_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B025_180525L13_exp180222_MS01_SCGE_AB20.2x36mers.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 B025_180525L13_exp180222_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B025_180525L13_exp180222_MS01_SCGE_AB20.2x36mers.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 B025_180525L13_exp180222_MS01_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B025_180525L13_exp180222_MS01_SCGE_AB20.1x36mers.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 B025_180525L13_exp180222_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B025_180525L13_exp180222_MS01_SCGE_AB20.2x36mers.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 B025_180525L13_exp180222_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B025_180525L13_exp180222_MS01_SCGE_AB20.2x36mers.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