python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_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 A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_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 A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_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 A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_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 A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_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 A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A001_180415LA_exp180227_MS1-MS99_ratio-0.0625_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 A002_180415LB_exp180227_MS1-MS99_ratio-0.25_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A002_180415LB_exp180227_MS1-MS99_ratio-0.25_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 A002_180415LB_exp180227_MS1-MS99_ratio-0.25_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A002_180415LB_exp180227_MS1-MS99_ratio-0.25_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 A002_180415LB_exp180227_MS1-MS99_ratio-0.25_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A002_180415LB_exp180227_MS1-MS99_ratio-0.25_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 A002_180415LB_exp180227_MS1-MS99_ratio-0.25_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A002_180415LB_exp180227_MS1-MS99_ratio-0.25_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 A002_180415LB_exp180227_MS1-MS99_ratio-0.25_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A002_180415LB_exp180227_MS1-MS99_ratio-0.25_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 A002_180415LB_exp180227_MS1-MS99_ratio-0.25_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A002_180415LB_exp180227_MS1-MS99_ratio-0.25_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 A003_180415LC_exp180227_MS1-MS99_ratio-0.50_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A003_180415LC_exp180227_MS1-MS99_ratio-0.50_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 A003_180415LC_exp180227_MS1-MS99_ratio-0.50_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A003_180415LC_exp180227_MS1-MS99_ratio-0.50_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 A003_180415LC_exp180227_MS1-MS99_ratio-0.50_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A003_180415LC_exp180227_MS1-MS99_ratio-0.50_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 A003_180415LC_exp180227_MS1-MS99_ratio-0.50_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A003_180415LC_exp180227_MS1-MS99_ratio-0.50_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 A003_180415LC_exp180227_MS1-MS99_ratio-0.50_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A003_180415LC_exp180227_MS1-MS99_ratio-0.50_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 A003_180415LC_exp180227_MS1-MS99_ratio-0.50_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A003_180415LC_exp180227_MS1-MS99_ratio-0.50_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 A004_180415LD_exp180227_MS1-MS99_ratio-1.00_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A004_180415LD_exp180227_MS1-MS99_ratio-1.00_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 A004_180415LD_exp180227_MS1-MS99_ratio-1.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A004_180415LD_exp180227_MS1-MS99_ratio-1.00_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 A004_180415LD_exp180227_MS1-MS99_ratio-1.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A004_180415LD_exp180227_MS1-MS99_ratio-1.00_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 A004_180415LD_exp180227_MS1-MS99_ratio-1.00_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A004_180415LD_exp180227_MS1-MS99_ratio-1.00_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 A004_180415LD_exp180227_MS1-MS99_ratio-1.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A004_180415LD_exp180227_MS1-MS99_ratio-1.00_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 A004_180415LD_exp180227_MS1-MS99_ratio-1.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A004_180415LD_exp180227_MS1-MS99_ratio-1.00_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 A005_180415LE_exp180227_MS1-MS99_ratio-2.00_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A005_180415LE_exp180227_MS1-MS99_ratio-2.00_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 A005_180415LE_exp180227_MS1-MS99_ratio-2.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A005_180415LE_exp180227_MS1-MS99_ratio-2.00_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 A005_180415LE_exp180227_MS1-MS99_ratio-2.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A005_180415LE_exp180227_MS1-MS99_ratio-2.00_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 A005_180415LE_exp180227_MS1-MS99_ratio-2.00_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A005_180415LE_exp180227_MS1-MS99_ratio-2.00_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 A005_180415LE_exp180227_MS1-MS99_ratio-2.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A005_180415LE_exp180227_MS1-MS99_ratio-2.00_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 A005_180415LE_exp180227_MS1-MS99_ratio-2.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A005_180415LE_exp180227_MS1-MS99_ratio-2.00_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 A006_180415LF_exp180227_MS1-MS99_ratio-4.00_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A006_180415LF_exp180227_MS1-MS99_ratio-4.00_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 A006_180415LF_exp180227_MS1-MS99_ratio-4.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A006_180415LF_exp180227_MS1-MS99_ratio-4.00_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 A006_180415LF_exp180227_MS1-MS99_ratio-4.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A006_180415LF_exp180227_MS1-MS99_ratio-4.00_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 A006_180415LF_exp180227_MS1-MS99_ratio-4.00_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A006_180415LF_exp180227_MS1-MS99_ratio-4.00_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 A006_180415LF_exp180227_MS1-MS99_ratio-4.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A006_180415LF_exp180227_MS1-MS99_ratio-4.00_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 A006_180415LF_exp180227_MS1-MS99_ratio-4.00_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A006_180415LF_exp180227_MS1-MS99_ratio-4.00_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 A007_180415LG_exp180227_MS1-MS99_ratio-16.0_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A007_180415LG_exp180227_MS1-MS99_ratio-16.0_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 A007_180415LG_exp180227_MS1-MS99_ratio-16.0_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A007_180415LG_exp180227_MS1-MS99_ratio-16.0_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 A007_180415LG_exp180227_MS1-MS99_ratio-16.0_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A007_180415LG_exp180227_MS1-MS99_ratio-16.0_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 A007_180415LG_exp180227_MS1-MS99_ratio-16.0_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A007_180415LG_exp180227_MS1-MS99_ratio-16.0_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 A007_180415LG_exp180227_MS1-MS99_ratio-16.0_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A007_180415LG_exp180227_MS1-MS99_ratio-16.0_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 A007_180415LG_exp180227_MS1-MS99_ratio-16.0_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A007_180415LG_exp180227_MS1-MS99_ratio-16.0_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 A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_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 A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_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 A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_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 A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_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 A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_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 A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A008_180415LA20_exp180227_MS1-MS99_ratio-0.0625_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_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 A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_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 A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_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 A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_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 A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_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 A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A009_180415LB20_exp180227_MS1-MS99_ratio-0.25_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_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 A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_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 A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_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 A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_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 A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_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 A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A010_180415LC20_exp180227_MS1-MS99_ratio-0.50_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_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 A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_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 A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_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 A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_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 A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_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 A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A011_180415LD20_exp180227_MS1-MS99_ratio-1.00_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_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 A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_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 A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_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 A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_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 A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_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 A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A012_180415LE20_exp180227_MS1-MS99_ratio-2.00_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_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 A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_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 A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_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 A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_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 A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_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 A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A013_180415LF20_exp180227_MS1-MS99_ratio-4.00_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_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 A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_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 A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_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 A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_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 A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_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 A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A014_180415LG20_exp180227_MS1-MS99_ratio-16.0_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_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 A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_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 A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_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 A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_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 A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_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 A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A015_180415LA01_exp180227_MS1-MS99_ratio-0.0625_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 A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_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 A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_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 A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_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 A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_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 A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_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 A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A016_180415LB01_exp180227_MS1-MS99_ratio-0.25_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 A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_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 A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_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 A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_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 A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_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 A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_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 A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A017_180415LC01_exp180227_MS1-MS99_ratio-0.50_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 A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_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 A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_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 A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_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 A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_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 A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_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 A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A018_180415LD01_exp180227_MS1-MS99_ratio-1.00_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 A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_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 A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_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 A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_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 A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_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 A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_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 A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A019_180415LE01_exp180227_MS1-MS99_ratio-2.00_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 A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_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 A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_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 A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_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 A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_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 A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_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 A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A020_180415LF01_exp180227_MS1-MS99_ratio-4.00_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 A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_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 A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_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 A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_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 A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_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 A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_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 A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A021_180415LG01_exp180227_MS1-MS99_ratio-16.0_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 A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.1x36mers.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 A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.2x36mers.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 A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.2x36mers.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 A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.1x36mers.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 A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.2x36mers.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 A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A022_180415LA04_exp180227_MS1-MS99_ratio-0.0625_AB04.2x36mers.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 A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.1x36mers.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 A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.2x36mers.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 A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.2x36mers.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 A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.1x36mers.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 A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.2x36mers.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 A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A023_180415LB04_exp180227_MS1-MS99_ratio-0.25_AB04.2x36mers.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 A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.1x36mers.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 A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.2x36mers.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 A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.2x36mers.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 A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.1x36mers.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 A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.2x36mers.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 A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A024_180415LC04_exp180227_MS1-MS99_ratio-0.50_AB04.2x36mers.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 A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.1x36mers.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 A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.2x36mers.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 A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.2x36mers.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 A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.1x36mers.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 A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.2x36mers.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 A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A025_180415LD04_exp180227_MS1-MS99_ratio-1.00_AB04.2x36mers.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 A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.1x36mers.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 A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.2x36mers.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 A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.2x36mers.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 A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.1x36mers.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 A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.2x36mers.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 A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A026_180415LE04_exp180227_MS1-MS99_ratio-2.00_AB04.2x36mers.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 A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.1x36mers.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 A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.2x36mers.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 A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.2x36mers.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 A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.1x36mers.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 A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.2x36mers.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 A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A027_180415LF04_exp180227_MS1-MS99_ratio-4.00_AB04.2x36mers.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 A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.1x36mers.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 A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.2x36mers.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 A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.2x36mers.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 A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.1x36mers.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 A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.2x36mers.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 A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A028_180415LG04_exp180227_MS1-MS99_ratio-16.0_AB04.2x36mers.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 A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_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 A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_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 A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_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 A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_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 A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_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 A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A029_180522L01_exp180413_MS204_SCGE-RAPA-00min_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 A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_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 A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_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 A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_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 A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_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 A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_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 A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A030_180522L02_exp180413_MS204_SCGE-RAPA-10min_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 A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_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 A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_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 A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_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 A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_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 A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_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 A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A031_180522L03_exp180413_MS204_SCGE-RAPA-20min_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 A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_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 A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_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 A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_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 A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_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 A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_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 A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A032_180522L04_exp180413_MS204_SCGE-RAPA-30min_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 A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_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 A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_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 A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_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 A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_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 A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_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 A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A033_180522L05_exp180413_MS204_SCGE-RAPA-60min_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 A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_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 A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_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 A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_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 A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_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 A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_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 A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A034_180522L06_exp180413_MS205_SCGE-RAPA-00min_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 A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_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 A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_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 A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_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 A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_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 A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_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 A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A035_180522L07_exp180413_MS205_SCGE-RAPA-10min_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 A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_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 A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_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 A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_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 A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_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 A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_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 A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A036_180522L08_exp180413_MS205_SCGE-RAPA-20min_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 A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_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 A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_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 A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_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 A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_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 A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_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 A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A037_180522L09_exp180413_MS205_SCGE-RAPA-30min_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 A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_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 A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_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 A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_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 A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_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 A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_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 A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A038_180522L10_exp180413_MS205_SCGE-RAPA-60min_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 A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_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 A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_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 A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_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 A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_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 A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_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 A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A039_180522L11_exp180413_MS204_SCGE-RAPA-00min_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 A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_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 A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_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 A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_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 A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_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 A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_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 A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A040_180522L12_exp180413_MS204_SCGE-RAPA-10min_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 A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_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 A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_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 A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_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 A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_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 A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_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 A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A041_180522L13_exp180413_MS204_SCGE-RAPA-20min_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 A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_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 A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_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 A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_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 A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_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 A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_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 A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A042_180522L14_exp180413_MS204_SCGE-RAPA-30min_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 A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_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 A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_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 A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_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 A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_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 A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_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 A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A043_180522L15_exp180413_MS204_SCGE-RAPA-60min_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 A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_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 A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_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 A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_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 A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_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 A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_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 A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A044_180522L16_exp180413_MS205_SCGE-RAPA-00min_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 A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_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 A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_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 A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_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 A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_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 A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_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 A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A045_180522L17_exp180413_MS205_SCGE-RAPA-10min_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 A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_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 A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_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 A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_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 A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_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 A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_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 A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A046_180522L18_exp180413_MS205_SCGE-RAPA-20min_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 A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_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 A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_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 A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_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 A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_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 A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_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 A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A047_180522L19_exp180413_MS205_SCGE-RAPA-30min_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 A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_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 A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_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 A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_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 A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_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 A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_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 A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A048_180522L20_exp180413_MS205_SCGE-RAPA-60min_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 A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_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 A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_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 A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_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 A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_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 A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_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 A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A049_180522L21_exp180413_MS204_SCGE-RAPA-00min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_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 A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_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 A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_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 A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_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 A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_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 A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A050_180522L22_exp180413_MS204_SCGE-RAPA-10min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_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 A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_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 A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_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 A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_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 A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_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 A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A051_180522L23_exp180413_MS204_SCGE-RAPA-20min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_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 A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_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 A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_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 A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_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 A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_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 A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A052_180522L24_exp180413_MS204_SCGE-RAPA-30min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_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 A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_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 A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_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 A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_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 A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_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 A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A053_180522L25_exp180413_MS204_SCGE-RAPA-60min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_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 A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_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 A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_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 A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_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 A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_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 A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A054_180522L26_exp180413_MS205_SCGE-RAPA-00min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_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 A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_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 A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_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 A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_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 A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_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 A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A055_180522L27_exp180413_MS205_SCGE-RAPA-10min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_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 A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_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 A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_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 A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_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 A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_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 A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A056_180522L28_exp180413_MS205_SCGE-RAPA-20min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_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 A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_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 A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_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 A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_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 A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_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 A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A057_180522L29_exp180413_MS205_SCGE-RAPA-30min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_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 A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_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 A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_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 A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_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 A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_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 A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A058_180522L30_exp180413_MS205_SCGE-RAPA-60min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A059_180531L01_exp180524_MS1_SCGE_OD0.1_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A059_180531L01_exp180524_MS1_SCGE_OD0.1_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 A059_180531L01_exp180524_MS1_SCGE_OD0.1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A059_180531L01_exp180524_MS1_SCGE_OD0.1_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 A059_180531L01_exp180524_MS1_SCGE_OD0.1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A059_180531L01_exp180524_MS1_SCGE_OD0.1_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 A059_180531L01_exp180524_MS1_SCGE_OD0.1_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A059_180531L01_exp180524_MS1_SCGE_OD0.1_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 A059_180531L01_exp180524_MS1_SCGE_OD0.1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A059_180531L01_exp180524_MS1_SCGE_OD0.1_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 A059_180531L01_exp180524_MS1_SCGE_OD0.1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A059_180531L01_exp180524_MS1_SCGE_OD0.1_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 A060_180531L02_exp180524_MS1_SCGE_OD0.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A060_180531L02_exp180524_MS1_SCGE_OD0.2_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 A060_180531L02_exp180524_MS1_SCGE_OD0.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A060_180531L02_exp180524_MS1_SCGE_OD0.2_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 A060_180531L02_exp180524_MS1_SCGE_OD0.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A060_180531L02_exp180524_MS1_SCGE_OD0.2_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 A060_180531L02_exp180524_MS1_SCGE_OD0.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A060_180531L02_exp180524_MS1_SCGE_OD0.2_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 A060_180531L02_exp180524_MS1_SCGE_OD0.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A060_180531L02_exp180524_MS1_SCGE_OD0.2_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 A060_180531L02_exp180524_MS1_SCGE_OD0.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A060_180531L02_exp180524_MS1_SCGE_OD0.2_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 A061_180531L03_exp180524_MS1_SCGE_OD0.3_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A061_180531L03_exp180524_MS1_SCGE_OD0.3_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 A061_180531L03_exp180524_MS1_SCGE_OD0.3_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A061_180531L03_exp180524_MS1_SCGE_OD0.3_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 A061_180531L03_exp180524_MS1_SCGE_OD0.3_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A061_180531L03_exp180524_MS1_SCGE_OD0.3_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 A061_180531L03_exp180524_MS1_SCGE_OD0.3_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A061_180531L03_exp180524_MS1_SCGE_OD0.3_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 A061_180531L03_exp180524_MS1_SCGE_OD0.3_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A061_180531L03_exp180524_MS1_SCGE_OD0.3_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 A061_180531L03_exp180524_MS1_SCGE_OD0.3_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A061_180531L03_exp180524_MS1_SCGE_OD0.3_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 A062_180531L04_exp180524_MS1_SCGE_OD0.4_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A062_180531L04_exp180524_MS1_SCGE_OD0.4_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 A062_180531L04_exp180524_MS1_SCGE_OD0.4_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A062_180531L04_exp180524_MS1_SCGE_OD0.4_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 A062_180531L04_exp180524_MS1_SCGE_OD0.4_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A062_180531L04_exp180524_MS1_SCGE_OD0.4_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 A062_180531L04_exp180524_MS1_SCGE_OD0.4_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A062_180531L04_exp180524_MS1_SCGE_OD0.4_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 A062_180531L04_exp180524_MS1_SCGE_OD0.4_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A062_180531L04_exp180524_MS1_SCGE_OD0.4_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 A062_180531L04_exp180524_MS1_SCGE_OD0.4_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A062_180531L04_exp180524_MS1_SCGE_OD0.4_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 A063_180531L05_exp180524_MS1_SCGE_OD0.5_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A063_180531L05_exp180524_MS1_SCGE_OD0.5_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 A063_180531L05_exp180524_MS1_SCGE_OD0.5_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A063_180531L05_exp180524_MS1_SCGE_OD0.5_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 A063_180531L05_exp180524_MS1_SCGE_OD0.5_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A063_180531L05_exp180524_MS1_SCGE_OD0.5_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 A063_180531L05_exp180524_MS1_SCGE_OD0.5_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A063_180531L05_exp180524_MS1_SCGE_OD0.5_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 A063_180531L05_exp180524_MS1_SCGE_OD0.5_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A063_180531L05_exp180524_MS1_SCGE_OD0.5_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 A063_180531L05_exp180524_MS1_SCGE_OD0.5_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A063_180531L05_exp180524_MS1_SCGE_OD0.5_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 A064_180531L06_exp180524_MS1_SCGE_OD0.6_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A064_180531L06_exp180524_MS1_SCGE_OD0.6_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 A064_180531L06_exp180524_MS1_SCGE_OD0.6_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A064_180531L06_exp180524_MS1_SCGE_OD0.6_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 A064_180531L06_exp180524_MS1_SCGE_OD0.6_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A064_180531L06_exp180524_MS1_SCGE_OD0.6_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 A064_180531L06_exp180524_MS1_SCGE_OD0.6_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A064_180531L06_exp180524_MS1_SCGE_OD0.6_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 A064_180531L06_exp180524_MS1_SCGE_OD0.6_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A064_180531L06_exp180524_MS1_SCGE_OD0.6_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 A064_180531L06_exp180524_MS1_SCGE_OD0.6_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A064_180531L06_exp180524_MS1_SCGE_OD0.6_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 A065_180531L07_exp180524_MS1_SCGE_OD0.1_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A065_180531L07_exp180524_MS1_SCGE_OD0.1_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 A065_180531L07_exp180524_MS1_SCGE_OD0.1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A065_180531L07_exp180524_MS1_SCGE_OD0.1_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 A065_180531L07_exp180524_MS1_SCGE_OD0.1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A065_180531L07_exp180524_MS1_SCGE_OD0.1_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 A065_180531L07_exp180524_MS1_SCGE_OD0.1_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A065_180531L07_exp180524_MS1_SCGE_OD0.1_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 A065_180531L07_exp180524_MS1_SCGE_OD0.1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A065_180531L07_exp180524_MS1_SCGE_OD0.1_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 A065_180531L07_exp180524_MS1_SCGE_OD0.1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A065_180531L07_exp180524_MS1_SCGE_OD0.1_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 A066_180531L08_exp180524_MS1_SCGE_OD0.2_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A066_180531L08_exp180524_MS1_SCGE_OD0.2_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 A066_180531L08_exp180524_MS1_SCGE_OD0.2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A066_180531L08_exp180524_MS1_SCGE_OD0.2_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 A066_180531L08_exp180524_MS1_SCGE_OD0.2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A066_180531L08_exp180524_MS1_SCGE_OD0.2_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 A066_180531L08_exp180524_MS1_SCGE_OD0.2_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A066_180531L08_exp180524_MS1_SCGE_OD0.2_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 A066_180531L08_exp180524_MS1_SCGE_OD0.2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A066_180531L08_exp180524_MS1_SCGE_OD0.2_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 A066_180531L08_exp180524_MS1_SCGE_OD0.2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A066_180531L08_exp180524_MS1_SCGE_OD0.2_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 A067_180531L09_exp180524_MS1_SCGE_OD0.3_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A067_180531L09_exp180524_MS1_SCGE_OD0.3_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 A067_180531L09_exp180524_MS1_SCGE_OD0.3_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A067_180531L09_exp180524_MS1_SCGE_OD0.3_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 A067_180531L09_exp180524_MS1_SCGE_OD0.3_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A067_180531L09_exp180524_MS1_SCGE_OD0.3_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 A067_180531L09_exp180524_MS1_SCGE_OD0.3_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A067_180531L09_exp180524_MS1_SCGE_OD0.3_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 A067_180531L09_exp180524_MS1_SCGE_OD0.3_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A067_180531L09_exp180524_MS1_SCGE_OD0.3_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 A067_180531L09_exp180524_MS1_SCGE_OD0.3_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A067_180531L09_exp180524_MS1_SCGE_OD0.3_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 A068_180531L10_exp180524_MS1_SCGE_OD0.4_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A068_180531L10_exp180524_MS1_SCGE_OD0.4_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 A068_180531L10_exp180524_MS1_SCGE_OD0.4_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A068_180531L10_exp180524_MS1_SCGE_OD0.4_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 A068_180531L10_exp180524_MS1_SCGE_OD0.4_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A068_180531L10_exp180524_MS1_SCGE_OD0.4_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 A068_180531L10_exp180524_MS1_SCGE_OD0.4_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A068_180531L10_exp180524_MS1_SCGE_OD0.4_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 A068_180531L10_exp180524_MS1_SCGE_OD0.4_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A068_180531L10_exp180524_MS1_SCGE_OD0.4_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 A068_180531L10_exp180524_MS1_SCGE_OD0.4_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A068_180531L10_exp180524_MS1_SCGE_OD0.4_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 A069_180531L11_exp180524_MS1_SCGE_OD0.5_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A069_180531L11_exp180524_MS1_SCGE_OD0.5_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 A069_180531L11_exp180524_MS1_SCGE_OD0.5_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A069_180531L11_exp180524_MS1_SCGE_OD0.5_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 A069_180531L11_exp180524_MS1_SCGE_OD0.5_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A069_180531L11_exp180524_MS1_SCGE_OD0.5_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 A069_180531L11_exp180524_MS1_SCGE_OD0.5_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A069_180531L11_exp180524_MS1_SCGE_OD0.5_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 A069_180531L11_exp180524_MS1_SCGE_OD0.5_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A069_180531L11_exp180524_MS1_SCGE_OD0.5_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 A069_180531L11_exp180524_MS1_SCGE_OD0.5_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A069_180531L11_exp180524_MS1_SCGE_OD0.5_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 A070_180531L12_exp180524_MS1_SCGE_OD0.6_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A070_180531L12_exp180524_MS1_SCGE_OD0.6_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 A070_180531L12_exp180524_MS1_SCGE_OD0.6_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A070_180531L12_exp180524_MS1_SCGE_OD0.6_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 A070_180531L12_exp180524_MS1_SCGE_OD0.6_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A070_180531L12_exp180524_MS1_SCGE_OD0.6_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 A070_180531L12_exp180524_MS1_SCGE_OD0.6_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A070_180531L12_exp180524_MS1_SCGE_OD0.6_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 A070_180531L12_exp180524_MS1_SCGE_OD0.6_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A070_180531L12_exp180524_MS1_SCGE_OD0.6_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 A070_180531L12_exp180524_MS1_SCGE_OD0.6_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A070_180531L12_exp180524_MS1_SCGE_OD0.6_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 A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.1x36mers.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 A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.2x36mers.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 A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.2x36mers.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 A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.1x36mers.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 A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.2x36mers.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 A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A071_180531L13_exp180524_MS1_SCGE_OD0.1_AB04.2x36mers.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 A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.1x36mers.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 A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.2x36mers.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 A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.2x36mers.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 A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.1x36mers.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 A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.2x36mers.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 A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A072_180531L14_exp180524_MS1_SCGE_OD0.2_AB04.2x36mers.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 A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.1x36mers.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 A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.2x36mers.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 A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.2x36mers.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 A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.1x36mers.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 A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.2x36mers.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 A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A073_180531L15_exp180524_MS1_SCGE_OD0.3_AB04.2x36mers.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 A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.1x36mers.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 A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.2x36mers.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 A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.2x36mers.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 A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.1x36mers.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 A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.2x36mers.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 A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A074_180531L16_exp180524_MS1_SCGE_OD0.4_AB04.2x36mers.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 A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.1x36mers.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 A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.2x36mers.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 A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.2x36mers.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 A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.1x36mers.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 A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.2x36mers.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 A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A075_180531L17_exp180524_MS1_SCGE_OD0.5_AB04.2x36mers.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 A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.1x36mers.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 A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.2x36mers.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 A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.2x36mers.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 A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.1x36mers.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 A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.2x36mers.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 A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A076_180531L18_exp180524_MS1_SCGE_OD0.6_AB04.2x36mers.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 A077_180531L19_exp180524_MS1_SCGE_OD0.1_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A077_180531L19_exp180524_MS1_SCGE_OD0.1_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 A077_180531L19_exp180524_MS1_SCGE_OD0.1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A077_180531L19_exp180524_MS1_SCGE_OD0.1_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 A077_180531L19_exp180524_MS1_SCGE_OD0.1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A077_180531L19_exp180524_MS1_SCGE_OD0.1_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 A077_180531L19_exp180524_MS1_SCGE_OD0.1_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A077_180531L19_exp180524_MS1_SCGE_OD0.1_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 A077_180531L19_exp180524_MS1_SCGE_OD0.1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A077_180531L19_exp180524_MS1_SCGE_OD0.1_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 A077_180531L19_exp180524_MS1_SCGE_OD0.1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A077_180531L19_exp180524_MS1_SCGE_OD0.1_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A078_180531L20_exp180524_MS1_SCGE_OD0.2_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A078_180531L20_exp180524_MS1_SCGE_OD0.2_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 A078_180531L20_exp180524_MS1_SCGE_OD0.2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A078_180531L20_exp180524_MS1_SCGE_OD0.2_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 A078_180531L20_exp180524_MS1_SCGE_OD0.2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A078_180531L20_exp180524_MS1_SCGE_OD0.2_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 A078_180531L20_exp180524_MS1_SCGE_OD0.2_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A078_180531L20_exp180524_MS1_SCGE_OD0.2_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 A078_180531L20_exp180524_MS1_SCGE_OD0.2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A078_180531L20_exp180524_MS1_SCGE_OD0.2_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 A078_180531L20_exp180524_MS1_SCGE_OD0.2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A078_180531L20_exp180524_MS1_SCGE_OD0.2_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A079_180531L21_exp180524_MS1_SCGE_OD0.3_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A079_180531L21_exp180524_MS1_SCGE_OD0.3_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 A079_180531L21_exp180524_MS1_SCGE_OD0.3_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A079_180531L21_exp180524_MS1_SCGE_OD0.3_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 A079_180531L21_exp180524_MS1_SCGE_OD0.3_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A079_180531L21_exp180524_MS1_SCGE_OD0.3_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 A079_180531L21_exp180524_MS1_SCGE_OD0.3_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A079_180531L21_exp180524_MS1_SCGE_OD0.3_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 A079_180531L21_exp180524_MS1_SCGE_OD0.3_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A079_180531L21_exp180524_MS1_SCGE_OD0.3_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 A079_180531L21_exp180524_MS1_SCGE_OD0.3_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A079_180531L21_exp180524_MS1_SCGE_OD0.3_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A080_180531L22_exp180524_MS1_SCGE_OD0.4_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A080_180531L22_exp180524_MS1_SCGE_OD0.4_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 A080_180531L22_exp180524_MS1_SCGE_OD0.4_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A080_180531L22_exp180524_MS1_SCGE_OD0.4_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 A080_180531L22_exp180524_MS1_SCGE_OD0.4_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A080_180531L22_exp180524_MS1_SCGE_OD0.4_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 A080_180531L22_exp180524_MS1_SCGE_OD0.4_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A080_180531L22_exp180524_MS1_SCGE_OD0.4_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 A080_180531L22_exp180524_MS1_SCGE_OD0.4_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A080_180531L22_exp180524_MS1_SCGE_OD0.4_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 A080_180531L22_exp180524_MS1_SCGE_OD0.4_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A080_180531L22_exp180524_MS1_SCGE_OD0.4_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A081_180531L23_exp180524_MS1_SCGE_OD0.5_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A081_180531L23_exp180524_MS1_SCGE_OD0.5_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 A081_180531L23_exp180524_MS1_SCGE_OD0.5_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A081_180531L23_exp180524_MS1_SCGE_OD0.5_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 A081_180531L23_exp180524_MS1_SCGE_OD0.5_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A081_180531L23_exp180524_MS1_SCGE_OD0.5_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 A081_180531L23_exp180524_MS1_SCGE_OD0.5_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A081_180531L23_exp180524_MS1_SCGE_OD0.5_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 A081_180531L23_exp180524_MS1_SCGE_OD0.5_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A081_180531L23_exp180524_MS1_SCGE_OD0.5_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 A081_180531L23_exp180524_MS1_SCGE_OD0.5_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A081_180531L23_exp180524_MS1_SCGE_OD0.5_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A082_180531L24_exp180524_MS1_SCGE_OD0.6_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A082_180531L24_exp180524_MS1_SCGE_OD0.6_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 A082_180531L24_exp180524_MS1_SCGE_OD0.6_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A082_180531L24_exp180524_MS1_SCGE_OD0.6_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 A082_180531L24_exp180524_MS1_SCGE_OD0.6_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A082_180531L24_exp180524_MS1_SCGE_OD0.6_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 A082_180531L24_exp180524_MS1_SCGE_OD0.6_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-A082_180531L24_exp180524_MS1_SCGE_OD0.6_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 A082_180531L24_exp180524_MS1_SCGE_OD0.6_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A082_180531L24_exp180524_MS1_SCGE_OD0.6_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 A082_180531L24_exp180524_MS1_SCGE_OD0.6_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-A082_180531L24_exp180524_MS1_SCGE_OD0.6_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B002_180525L02_exp180222_MS80_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B002_180525L02_exp180222_MS80_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 B002_180525L02_exp180222_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B002_180525L02_exp180222_MS80_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 B002_180525L02_exp180222_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B002_180525L02_exp180222_MS80_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 B002_180525L02_exp180222_MS80_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B002_180525L02_exp180222_MS80_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 B002_180525L02_exp180222_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B002_180525L02_exp180222_MS80_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 B002_180525L02_exp180222_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B002_180525L02_exp180222_MS80_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 B003_180525L03_exp180222_MS81_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B003_180525L03_exp180222_MS81_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 B003_180525L03_exp180222_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B003_180525L03_exp180222_MS81_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 B003_180525L03_exp180222_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B003_180525L03_exp180222_MS81_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 B003_180525L03_exp180222_MS81_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B003_180525L03_exp180222_MS81_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 B003_180525L03_exp180222_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B003_180525L03_exp180222_MS81_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 B003_180525L03_exp180222_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B003_180525L03_exp180222_MS81_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 B004_180529L01_exp180227_MS63_SCGE-00nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B004_180529L01_exp180227_MS63_SCGE-00nM-BE_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 B004_180529L01_exp180227_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B004_180529L01_exp180227_MS63_SCGE-00nM-BE_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 B004_180529L01_exp180227_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B004_180529L01_exp180227_MS63_SCGE-00nM-BE_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 B004_180529L01_exp180227_MS63_SCGE-00nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B004_180529L01_exp180227_MS63_SCGE-00nM-BE_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 B004_180529L01_exp180227_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B004_180529L01_exp180227_MS63_SCGE-00nM-BE_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 B004_180529L01_exp180227_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B004_180529L01_exp180227_MS63_SCGE-00nM-BE_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 B005_180529L02_exp180227_MS63_SCGE-10nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B005_180529L02_exp180227_MS63_SCGE-10nM-BE_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 B005_180529L02_exp180227_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B005_180529L02_exp180227_MS63_SCGE-10nM-BE_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 B005_180529L02_exp180227_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B005_180529L02_exp180227_MS63_SCGE-10nM-BE_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 B005_180529L02_exp180227_MS63_SCGE-10nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B005_180529L02_exp180227_MS63_SCGE-10nM-BE_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 B005_180529L02_exp180227_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B005_180529L02_exp180227_MS63_SCGE-10nM-BE_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 B005_180529L02_exp180227_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B005_180529L02_exp180227_MS63_SCGE-10nM-BE_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 B006_180529L03_exp180227_MS63_SCGE-30nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B006_180529L03_exp180227_MS63_SCGE-30nM-BE_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 B006_180529L03_exp180227_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B006_180529L03_exp180227_MS63_SCGE-30nM-BE_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 B006_180529L03_exp180227_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B006_180529L03_exp180227_MS63_SCGE-30nM-BE_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 B006_180529L03_exp180227_MS63_SCGE-30nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B006_180529L03_exp180227_MS63_SCGE-30nM-BE_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 B006_180529L03_exp180227_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B006_180529L03_exp180227_MS63_SCGE-30nM-BE_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 B006_180529L03_exp180227_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B006_180529L03_exp180227_MS63_SCGE-30nM-BE_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 B008_180525L05_exp180222_MS80_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B008_180525L05_exp180222_MS80_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 B008_180525L05_exp180222_MS80_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B008_180525L05_exp180222_MS80_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 B008_180525L05_exp180222_MS80_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B008_180525L05_exp180222_MS80_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 B008_180525L05_exp180222_MS80_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B008_180525L05_exp180222_MS80_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 B008_180525L05_exp180222_MS80_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B008_180525L05_exp180222_MS80_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 B008_180525L05_exp180222_MS80_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B008_180525L05_exp180222_MS80_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 B009_180525L06_exp180222_MS81_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B009_180525L06_exp180222_MS81_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 B009_180525L06_exp180222_MS81_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B009_180525L06_exp180222_MS81_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 B009_180525L06_exp180222_MS81_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B009_180525L06_exp180222_MS81_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 B009_180525L06_exp180222_MS81_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B009_180525L06_exp180222_MS81_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 B009_180525L06_exp180222_MS81_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B009_180525L06_exp180222_MS81_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 B009_180525L06_exp180222_MS81_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B009_180525L06_exp180222_MS81_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 B010_180529L04_exp180227_MS63_SCGE-00nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B010_180529L04_exp180227_MS63_SCGE-00nM-BE_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 B010_180529L04_exp180227_MS63_SCGE-00nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B010_180529L04_exp180227_MS63_SCGE-00nM-BE_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 B010_180529L04_exp180227_MS63_SCGE-00nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B010_180529L04_exp180227_MS63_SCGE-00nM-BE_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 B010_180529L04_exp180227_MS63_SCGE-00nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B010_180529L04_exp180227_MS63_SCGE-00nM-BE_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 B010_180529L04_exp180227_MS63_SCGE-00nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B010_180529L04_exp180227_MS63_SCGE-00nM-BE_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 B010_180529L04_exp180227_MS63_SCGE-00nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B010_180529L04_exp180227_MS63_SCGE-00nM-BE_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 B011_180529L05_exp180227_MS63_SCGE-10nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B011_180529L05_exp180227_MS63_SCGE-10nM-BE_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 B011_180529L05_exp180227_MS63_SCGE-10nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B011_180529L05_exp180227_MS63_SCGE-10nM-BE_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 B011_180529L05_exp180227_MS63_SCGE-10nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B011_180529L05_exp180227_MS63_SCGE-10nM-BE_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 B011_180529L05_exp180227_MS63_SCGE-10nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B011_180529L05_exp180227_MS63_SCGE-10nM-BE_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 B011_180529L05_exp180227_MS63_SCGE-10nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B011_180529L05_exp180227_MS63_SCGE-10nM-BE_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 B011_180529L05_exp180227_MS63_SCGE-10nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B011_180529L05_exp180227_MS63_SCGE-10nM-BE_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 B012_180529L06_exp180227_MS63_SCGE-30nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B012_180529L06_exp180227_MS63_SCGE-30nM-BE_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 B012_180529L06_exp180227_MS63_SCGE-30nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B012_180529L06_exp180227_MS63_SCGE-30nM-BE_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 B012_180529L06_exp180227_MS63_SCGE-30nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B012_180529L06_exp180227_MS63_SCGE-30nM-BE_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 B012_180529L06_exp180227_MS63_SCGE-30nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B012_180529L06_exp180227_MS63_SCGE-30nM-BE_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 B012_180529L06_exp180227_MS63_SCGE-30nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B012_180529L06_exp180227_MS63_SCGE-30nM-BE_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 B012_180529L06_exp180227_MS63_SCGE-30nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B012_180529L06_exp180227_MS63_SCGE-30nM-BE_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 B014_180525L08_exp180222_MS80_SCGE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B014_180525L08_exp180222_MS80_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 B014_180525L08_exp180222_MS80_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B014_180525L08_exp180222_MS80_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 B014_180525L08_exp180222_MS80_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B014_180525L08_exp180222_MS80_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 B014_180525L08_exp180222_MS80_SCGE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B014_180525L08_exp180222_MS80_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 B014_180525L08_exp180222_MS80_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B014_180525L08_exp180222_MS80_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 B014_180525L08_exp180222_MS80_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B014_180525L08_exp180222_MS80_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 B015_180525L09_exp180222_MS81_SCGE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B015_180525L09_exp180222_MS81_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 B015_180525L09_exp180222_MS81_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B015_180525L09_exp180222_MS81_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 B015_180525L09_exp180222_MS81_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B015_180525L09_exp180222_MS81_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 B015_180525L09_exp180222_MS81_SCGE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B015_180525L09_exp180222_MS81_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 B015_180525L09_exp180222_MS81_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B015_180525L09_exp180222_MS81_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 B015_180525L09_exp180222_MS81_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B015_180525L09_exp180222_MS81_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 B016_180529L07_exp180227_MS63_SCGE-00nM-BE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B016_180529L07_exp180227_MS63_SCGE-00nM-BE_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 B016_180529L07_exp180227_MS63_SCGE-00nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B016_180529L07_exp180227_MS63_SCGE-00nM-BE_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 B016_180529L07_exp180227_MS63_SCGE-00nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B016_180529L07_exp180227_MS63_SCGE-00nM-BE_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 B016_180529L07_exp180227_MS63_SCGE-00nM-BE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B016_180529L07_exp180227_MS63_SCGE-00nM-BE_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 B016_180529L07_exp180227_MS63_SCGE-00nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B016_180529L07_exp180227_MS63_SCGE-00nM-BE_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 B016_180529L07_exp180227_MS63_SCGE-00nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B016_180529L07_exp180227_MS63_SCGE-00nM-BE_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 B017_180529L08_exp180227_MS63_SCGE-10nM-BE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B017_180529L08_exp180227_MS63_SCGE-10nM-BE_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 B017_180529L08_exp180227_MS63_SCGE-10nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B017_180529L08_exp180227_MS63_SCGE-10nM-BE_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 B017_180529L08_exp180227_MS63_SCGE-10nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B017_180529L08_exp180227_MS63_SCGE-10nM-BE_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 B017_180529L08_exp180227_MS63_SCGE-10nM-BE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B017_180529L08_exp180227_MS63_SCGE-10nM-BE_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 B017_180529L08_exp180227_MS63_SCGE-10nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B017_180529L08_exp180227_MS63_SCGE-10nM-BE_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 B017_180529L08_exp180227_MS63_SCGE-10nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B017_180529L08_exp180227_MS63_SCGE-10nM-BE_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 B018_180529L09_exp180227_MS63_SCGE-30nM-BE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B018_180529L09_exp180227_MS63_SCGE-30nM-BE_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 B018_180529L09_exp180227_MS63_SCGE-30nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B018_180529L09_exp180227_MS63_SCGE-30nM-BE_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 B018_180529L09_exp180227_MS63_SCGE-30nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B018_180529L09_exp180227_MS63_SCGE-30nM-BE_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 B018_180529L09_exp180227_MS63_SCGE-30nM-BE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B018_180529L09_exp180227_MS63_SCGE-30nM-BE_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 B018_180529L09_exp180227_MS63_SCGE-30nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B018_180529L09_exp180227_MS63_SCGE-30nM-BE_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 B018_180529L09_exp180227_MS63_SCGE-30nM-BE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B018_180529L09_exp180227_MS63_SCGE-30nM-BE_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 B020_180525L11_exp180222_MS80_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B020_180525L11_exp180222_MS80_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 B020_180525L11_exp180222_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B020_180525L11_exp180222_MS80_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 B020_180525L11_exp180222_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B020_180525L11_exp180222_MS80_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 B020_180525L11_exp180222_MS80_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B020_180525L11_exp180222_MS80_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 B020_180525L11_exp180222_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B020_180525L11_exp180222_MS80_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 B020_180525L11_exp180222_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B020_180525L11_exp180222_MS80_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 B021_180525L12_exp180222_MS81_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B021_180525L12_exp180222_MS81_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 B021_180525L12_exp180222_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B021_180525L12_exp180222_MS81_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 B021_180525L12_exp180222_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B021_180525L12_exp180222_MS81_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 B021_180525L12_exp180222_MS81_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B021_180525L12_exp180222_MS81_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 B021_180525L12_exp180222_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B021_180525L12_exp180222_MS81_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 B021_180525L12_exp180222_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B021_180525L12_exp180222_MS81_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 B022_180529L10_exp180227_MS63_SCGE-00nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B022_180529L10_exp180227_MS63_SCGE-00nM-BE_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 B022_180529L10_exp180227_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B022_180529L10_exp180227_MS63_SCGE-00nM-BE_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 B022_180529L10_exp180227_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B022_180529L10_exp180227_MS63_SCGE-00nM-BE_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 B022_180529L10_exp180227_MS63_SCGE-00nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B022_180529L10_exp180227_MS63_SCGE-00nM-BE_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 B022_180529L10_exp180227_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B022_180529L10_exp180227_MS63_SCGE-00nM-BE_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 B022_180529L10_exp180227_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B022_180529L10_exp180227_MS63_SCGE-00nM-BE_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 B023_180529L11_exp180227_MS63_SCGE-10nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B023_180529L11_exp180227_MS63_SCGE-10nM-BE_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 B023_180529L11_exp180227_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B023_180529L11_exp180227_MS63_SCGE-10nM-BE_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 B023_180529L11_exp180227_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B023_180529L11_exp180227_MS63_SCGE-10nM-BE_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 B023_180529L11_exp180227_MS63_SCGE-10nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B023_180529L11_exp180227_MS63_SCGE-10nM-BE_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 B023_180529L11_exp180227_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B023_180529L11_exp180227_MS63_SCGE-10nM-BE_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 B023_180529L11_exp180227_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B023_180529L11_exp180227_MS63_SCGE-10nM-BE_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 B024_180529L12_exp180227_MS63_SCGE-30nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B024_180529L12_exp180227_MS63_SCGE-30nM-BE_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 B024_180529L12_exp180227_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B024_180529L12_exp180227_MS63_SCGE-30nM-BE_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 B024_180529L12_exp180227_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B024_180529L12_exp180227_MS63_SCGE-30nM-BE_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 B024_180529L12_exp180227_MS63_SCGE-30nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B024_180529L12_exp180227_MS63_SCGE-30nM-BE_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 B024_180529L12_exp180227_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B024_180529L12_exp180227_MS63_SCGE-30nM-BE_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 B024_180529L12_exp180227_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B024_180529L12_exp180227_MS63_SCGE-30nM-BE_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 B026_180525L14_exp180222_MS80_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B026_180525L14_exp180222_MS80_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 B026_180525L14_exp180222_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B026_180525L14_exp180222_MS80_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 B026_180525L14_exp180222_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B026_180525L14_exp180222_MS80_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 B026_180525L14_exp180222_MS80_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B026_180525L14_exp180222_MS80_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 B026_180525L14_exp180222_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B026_180525L14_exp180222_MS80_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 B026_180525L14_exp180222_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B026_180525L14_exp180222_MS80_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B027_180525L15_exp180222_MS81_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B027_180525L15_exp180222_MS81_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 B027_180525L15_exp180222_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B027_180525L15_exp180222_MS81_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 B027_180525L15_exp180222_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B027_180525L15_exp180222_MS81_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 B027_180525L15_exp180222_MS81_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B027_180525L15_exp180222_MS81_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 B027_180525L15_exp180222_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B027_180525L15_exp180222_MS81_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 B027_180525L15_exp180222_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B027_180525L15_exp180222_MS81_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B028_180529L13_exp180227_MS63_SCGE-00nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B028_180529L13_exp180227_MS63_SCGE-00nM-BE_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 B028_180529L13_exp180227_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B028_180529L13_exp180227_MS63_SCGE-00nM-BE_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 B028_180529L13_exp180227_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B028_180529L13_exp180227_MS63_SCGE-00nM-BE_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 B028_180529L13_exp180227_MS63_SCGE-00nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B028_180529L13_exp180227_MS63_SCGE-00nM-BE_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 B028_180529L13_exp180227_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B028_180529L13_exp180227_MS63_SCGE-00nM-BE_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 B028_180529L13_exp180227_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B028_180529L13_exp180227_MS63_SCGE-00nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B029_180529L14_exp180227_MS63_SCGE-10nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B029_180529L14_exp180227_MS63_SCGE-10nM-BE_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 B029_180529L14_exp180227_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B029_180529L14_exp180227_MS63_SCGE-10nM-BE_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 B029_180529L14_exp180227_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B029_180529L14_exp180227_MS63_SCGE-10nM-BE_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 B029_180529L14_exp180227_MS63_SCGE-10nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B029_180529L14_exp180227_MS63_SCGE-10nM-BE_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 B029_180529L14_exp180227_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B029_180529L14_exp180227_MS63_SCGE-10nM-BE_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 B029_180529L14_exp180227_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B029_180529L14_exp180227_MS63_SCGE-10nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B030_180529L15_exp180227_MS63_SCGE-30nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B030_180529L15_exp180227_MS63_SCGE-30nM-BE_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 B030_180529L15_exp180227_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B030_180529L15_exp180227_MS63_SCGE-30nM-BE_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 B030_180529L15_exp180227_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B030_180529L15_exp180227_MS63_SCGE-30nM-BE_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 B030_180529L15_exp180227_MS63_SCGE-30nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B030_180529L15_exp180227_MS63_SCGE-30nM-BE_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 B030_180529L15_exp180227_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B030_180529L15_exp180227_MS63_SCGE-30nM-BE_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 B030_180529L15_exp180227_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B030_180529L15_exp180227_MS63_SCGE-30nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B031_180718L01_exp180222_MS01_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B031_180718L01_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 B031_180718L01_exp180222_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B031_180718L01_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 B031_180718L01_exp180222_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B031_180718L01_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 B031_180718L01_exp180222_MS01_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B031_180718L01_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 B031_180718L01_exp180222_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B031_180718L01_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 B031_180718L01_exp180222_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B031_180718L01_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 B032_180718L06_exp180222_MS80_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B032_180718L06_exp180222_MS80_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 B032_180718L06_exp180222_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B032_180718L06_exp180222_MS80_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 B032_180718L06_exp180222_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B032_180718L06_exp180222_MS80_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 B032_180718L06_exp180222_MS80_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B032_180718L06_exp180222_MS80_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 B032_180718L06_exp180222_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B032_180718L06_exp180222_MS80_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 B032_180718L06_exp180222_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B032_180718L06_exp180222_MS80_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 B033_180718L11_exp180222_MS81_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B033_180718L11_exp180222_MS81_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 B033_180718L11_exp180222_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B033_180718L11_exp180222_MS81_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 B033_180718L11_exp180222_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B033_180718L11_exp180222_MS81_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 B033_180718L11_exp180222_MS81_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B033_180718L11_exp180222_MS81_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 B033_180718L11_exp180222_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B033_180718L11_exp180222_MS81_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 B033_180718L11_exp180222_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B033_180718L11_exp180222_MS81_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 B034_180718L16_exp180227_MS63_SCGE-00nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B034_180718L16_exp180227_MS63_SCGE-00nM-BE_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 B034_180718L16_exp180227_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B034_180718L16_exp180227_MS63_SCGE-00nM-BE_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 B034_180718L16_exp180227_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B034_180718L16_exp180227_MS63_SCGE-00nM-BE_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 B034_180718L16_exp180227_MS63_SCGE-00nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B034_180718L16_exp180227_MS63_SCGE-00nM-BE_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 B034_180718L16_exp180227_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B034_180718L16_exp180227_MS63_SCGE-00nM-BE_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 B034_180718L16_exp180227_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B034_180718L16_exp180227_MS63_SCGE-00nM-BE_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 B035_180718L21_exp180227_MS63_SCGE-10nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B035_180718L21_exp180227_MS63_SCGE-10nM-BE_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 B035_180718L21_exp180227_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B035_180718L21_exp180227_MS63_SCGE-10nM-BE_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 B035_180718L21_exp180227_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B035_180718L21_exp180227_MS63_SCGE-10nM-BE_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 B035_180718L21_exp180227_MS63_SCGE-10nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B035_180718L21_exp180227_MS63_SCGE-10nM-BE_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 B035_180718L21_exp180227_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B035_180718L21_exp180227_MS63_SCGE-10nM-BE_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 B035_180718L21_exp180227_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B035_180718L21_exp180227_MS63_SCGE-10nM-BE_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 B036_180718L26_exp180227_MS63_SCGE-30nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B036_180718L26_exp180227_MS63_SCGE-30nM-BE_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 B036_180718L26_exp180227_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B036_180718L26_exp180227_MS63_SCGE-30nM-BE_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 B036_180718L26_exp180227_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B036_180718L26_exp180227_MS63_SCGE-30nM-BE_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 B036_180718L26_exp180227_MS63_SCGE-30nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B036_180718L26_exp180227_MS63_SCGE-30nM-BE_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 B036_180718L26_exp180227_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B036_180718L26_exp180227_MS63_SCGE-30nM-BE_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 B036_180718L26_exp180227_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B036_180718L26_exp180227_MS63_SCGE-30nM-BE_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 B037_180718L02_exp180222_MS01_SCGE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B037_180718L02_exp180222_MS01_SCGE_input-2.1x36mers.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 B037_180718L02_exp180222_MS01_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B037_180718L02_exp180222_MS01_SCGE_input-2.2x36mers.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 B037_180718L02_exp180222_MS01_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B037_180718L02_exp180222_MS01_SCGE_input-2.2x36mers.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 B037_180718L02_exp180222_MS01_SCGE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B037_180718L02_exp180222_MS01_SCGE_input-2.1x36mers.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 B037_180718L02_exp180222_MS01_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B037_180718L02_exp180222_MS01_SCGE_input-2.2x36mers.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 B037_180718L02_exp180222_MS01_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B037_180718L02_exp180222_MS01_SCGE_input-2.2x36mers.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 B038_180718L07_exp180222_MS80_SCGE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B038_180718L07_exp180222_MS80_SCGE_input-2.1x36mers.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 B038_180718L07_exp180222_MS80_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B038_180718L07_exp180222_MS80_SCGE_input-2.2x36mers.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 B038_180718L07_exp180222_MS80_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B038_180718L07_exp180222_MS80_SCGE_input-2.2x36mers.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 B038_180718L07_exp180222_MS80_SCGE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B038_180718L07_exp180222_MS80_SCGE_input-2.1x36mers.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 B038_180718L07_exp180222_MS80_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B038_180718L07_exp180222_MS80_SCGE_input-2.2x36mers.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 B038_180718L07_exp180222_MS80_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B038_180718L07_exp180222_MS80_SCGE_input-2.2x36mers.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 B039_180718L12_exp180222_MS81_SCGE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B039_180718L12_exp180222_MS81_SCGE_input-2.1x36mers.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 B039_180718L12_exp180222_MS81_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B039_180718L12_exp180222_MS81_SCGE_input-2.2x36mers.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 B039_180718L12_exp180222_MS81_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B039_180718L12_exp180222_MS81_SCGE_input-2.2x36mers.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 B039_180718L12_exp180222_MS81_SCGE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B039_180718L12_exp180222_MS81_SCGE_input-2.1x36mers.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 B039_180718L12_exp180222_MS81_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B039_180718L12_exp180222_MS81_SCGE_input-2.2x36mers.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 B039_180718L12_exp180222_MS81_SCGE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B039_180718L12_exp180222_MS81_SCGE_input-2.2x36mers.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 B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.1x36mers.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 B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.2x36mers.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 B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.2x36mers.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 B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.1x36mers.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 B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.2x36mers.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 B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B040_180718L17_exp180227_MS63_SCGE-00nM-BE_input-2.2x36mers.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 B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.1x36mers.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 B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.2x36mers.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 B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.2x36mers.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 B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.1x36mers.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 B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.2x36mers.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 B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B041_180718L22_exp180227_MS63_SCGE-10nM-BE_input-2.2x36mers.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 B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.1x36mers.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 B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.2x36mers.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 B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.2x36mers.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 B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.1x36mers.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 B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.2x36mers.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 B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B042_180718L27_exp180227_MS63_SCGE-30nM-BE_input-2.2x36mers.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 B043_180718L03_exp180222_MS01_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B043_180718L03_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 B043_180718L03_exp180222_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B043_180718L03_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 B043_180718L03_exp180222_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B043_180718L03_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 B043_180718L03_exp180222_MS01_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B043_180718L03_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 B043_180718L03_exp180222_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B043_180718L03_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 B043_180718L03_exp180222_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B043_180718L03_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 B044_180718L08_exp180222_MS80_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B044_180718L08_exp180222_MS80_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 B044_180718L08_exp180222_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B044_180718L08_exp180222_MS80_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 B044_180718L08_exp180222_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B044_180718L08_exp180222_MS80_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 B044_180718L08_exp180222_MS80_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B044_180718L08_exp180222_MS80_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 B044_180718L08_exp180222_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B044_180718L08_exp180222_MS80_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 B044_180718L08_exp180222_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B044_180718L08_exp180222_MS80_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 B045_180718L13_exp180222_MS81_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B045_180718L13_exp180222_MS81_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 B045_180718L13_exp180222_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B045_180718L13_exp180222_MS81_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 B045_180718L13_exp180222_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B045_180718L13_exp180222_MS81_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 B045_180718L13_exp180222_MS81_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B045_180718L13_exp180222_MS81_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 B045_180718L13_exp180222_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B045_180718L13_exp180222_MS81_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 B045_180718L13_exp180222_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B045_180718L13_exp180222_MS81_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 B046_180718L18_exp180227_MS63_SCGE-00nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B046_180718L18_exp180227_MS63_SCGE-00nM-BE_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 B046_180718L18_exp180227_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B046_180718L18_exp180227_MS63_SCGE-00nM-BE_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 B046_180718L18_exp180227_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B046_180718L18_exp180227_MS63_SCGE-00nM-BE_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 B046_180718L18_exp180227_MS63_SCGE-00nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B046_180718L18_exp180227_MS63_SCGE-00nM-BE_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 B046_180718L18_exp180227_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B046_180718L18_exp180227_MS63_SCGE-00nM-BE_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 B046_180718L18_exp180227_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B046_180718L18_exp180227_MS63_SCGE-00nM-BE_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 B047_180718L23_exp180227_MS63_SCGE-10nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B047_180718L23_exp180227_MS63_SCGE-10nM-BE_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 B047_180718L23_exp180227_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B047_180718L23_exp180227_MS63_SCGE-10nM-BE_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 B047_180718L23_exp180227_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B047_180718L23_exp180227_MS63_SCGE-10nM-BE_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 B047_180718L23_exp180227_MS63_SCGE-10nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B047_180718L23_exp180227_MS63_SCGE-10nM-BE_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 B047_180718L23_exp180227_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B047_180718L23_exp180227_MS63_SCGE-10nM-BE_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 B047_180718L23_exp180227_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B047_180718L23_exp180227_MS63_SCGE-10nM-BE_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 B048_180718L28_exp180227_MS63_SCGE-30nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B048_180718L28_exp180227_MS63_SCGE-30nM-BE_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 B048_180718L28_exp180227_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B048_180718L28_exp180227_MS63_SCGE-30nM-BE_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 B048_180718L28_exp180227_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B048_180718L28_exp180227_MS63_SCGE-30nM-BE_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 B048_180718L28_exp180227_MS63_SCGE-30nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B048_180718L28_exp180227_MS63_SCGE-30nM-BE_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 B048_180718L28_exp180227_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B048_180718L28_exp180227_MS63_SCGE-30nM-BE_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 B048_180718L28_exp180227_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B048_180718L28_exp180227_MS63_SCGE-30nM-BE_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 B049_180718L04_exp180222_MS01_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B049_180718L04_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 B049_180718L04_exp180222_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B049_180718L04_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 B049_180718L04_exp180222_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B049_180718L04_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 B049_180718L04_exp180222_MS01_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B049_180718L04_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 B049_180718L04_exp180222_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B049_180718L04_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 B049_180718L04_exp180222_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B049_180718L04_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B050_180718L09_exp180222_MS80_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B050_180718L09_exp180222_MS80_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 B050_180718L09_exp180222_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B050_180718L09_exp180222_MS80_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 B050_180718L09_exp180222_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B050_180718L09_exp180222_MS80_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 B050_180718L09_exp180222_MS80_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B050_180718L09_exp180222_MS80_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 B050_180718L09_exp180222_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B050_180718L09_exp180222_MS80_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 B050_180718L09_exp180222_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B050_180718L09_exp180222_MS80_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B051_180718L14_exp180222_MS81_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B051_180718L14_exp180222_MS81_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 B051_180718L14_exp180222_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B051_180718L14_exp180222_MS81_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 B051_180718L14_exp180222_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B051_180718L14_exp180222_MS81_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 B051_180718L14_exp180222_MS81_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B051_180718L14_exp180222_MS81_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 B051_180718L14_exp180222_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B051_180718L14_exp180222_MS81_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 B051_180718L14_exp180222_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B051_180718L14_exp180222_MS81_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B052_180718L19_exp180227_MS63_SCGE-00nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B052_180718L19_exp180227_MS63_SCGE-00nM-BE_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 B052_180718L19_exp180227_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B052_180718L19_exp180227_MS63_SCGE-00nM-BE_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 B052_180718L19_exp180227_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B052_180718L19_exp180227_MS63_SCGE-00nM-BE_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 B052_180718L19_exp180227_MS63_SCGE-00nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B052_180718L19_exp180227_MS63_SCGE-00nM-BE_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 B052_180718L19_exp180227_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B052_180718L19_exp180227_MS63_SCGE-00nM-BE_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 B052_180718L19_exp180227_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B052_180718L19_exp180227_MS63_SCGE-00nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B053_180718L24_exp180227_MS63_SCGE-10nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B053_180718L24_exp180227_MS63_SCGE-10nM-BE_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 B053_180718L24_exp180227_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B053_180718L24_exp180227_MS63_SCGE-10nM-BE_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 B053_180718L24_exp180227_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B053_180718L24_exp180227_MS63_SCGE-10nM-BE_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 B053_180718L24_exp180227_MS63_SCGE-10nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B053_180718L24_exp180227_MS63_SCGE-10nM-BE_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 B053_180718L24_exp180227_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B053_180718L24_exp180227_MS63_SCGE-10nM-BE_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 B053_180718L24_exp180227_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B053_180718L24_exp180227_MS63_SCGE-10nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B054_180718L29_exp180227_MS63_SCGE-30nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B054_180718L29_exp180227_MS63_SCGE-30nM-BE_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 B054_180718L29_exp180227_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B054_180718L29_exp180227_MS63_SCGE-30nM-BE_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 B054_180718L29_exp180227_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B054_180718L29_exp180227_MS63_SCGE-30nM-BE_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 B054_180718L29_exp180227_MS63_SCGE-30nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B054_180718L29_exp180227_MS63_SCGE-30nM-BE_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 B054_180718L29_exp180227_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B054_180718L29_exp180227_MS63_SCGE-30nM-BE_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 B054_180718L29_exp180227_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B054_180718L29_exp180227_MS63_SCGE-30nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B055_180718L05_exp180222_MS01_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B055_180718L05_exp180222_MS01_SCGE_AB21.1x36mers.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 B055_180718L05_exp180222_MS01_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B055_180718L05_exp180222_MS01_SCGE_AB21.2x36mers.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 B055_180718L05_exp180222_MS01_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B055_180718L05_exp180222_MS01_SCGE_AB21.2x36mers.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 B055_180718L05_exp180222_MS01_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B055_180718L05_exp180222_MS01_SCGE_AB21.1x36mers.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 B055_180718L05_exp180222_MS01_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B055_180718L05_exp180222_MS01_SCGE_AB21.2x36mers.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 B055_180718L05_exp180222_MS01_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B055_180718L05_exp180222_MS01_SCGE_AB21.2x36mers.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 B056_180718L10_exp180222_MS80_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B056_180718L10_exp180222_MS80_SCGE_AB21.1x36mers.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 B056_180718L10_exp180222_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B056_180718L10_exp180222_MS80_SCGE_AB21.2x36mers.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 B056_180718L10_exp180222_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B056_180718L10_exp180222_MS80_SCGE_AB21.2x36mers.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 B056_180718L10_exp180222_MS80_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B056_180718L10_exp180222_MS80_SCGE_AB21.1x36mers.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 B056_180718L10_exp180222_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B056_180718L10_exp180222_MS80_SCGE_AB21.2x36mers.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 B056_180718L10_exp180222_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B056_180718L10_exp180222_MS80_SCGE_AB21.2x36mers.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 B057_180718L15_exp180222_MS81_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B057_180718L15_exp180222_MS81_SCGE_AB21.1x36mers.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 B057_180718L15_exp180222_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B057_180718L15_exp180222_MS81_SCGE_AB21.2x36mers.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 B057_180718L15_exp180222_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B057_180718L15_exp180222_MS81_SCGE_AB21.2x36mers.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 B057_180718L15_exp180222_MS81_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B057_180718L15_exp180222_MS81_SCGE_AB21.1x36mers.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 B057_180718L15_exp180222_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B057_180718L15_exp180222_MS81_SCGE_AB21.2x36mers.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 B057_180718L15_exp180222_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B057_180718L15_exp180222_MS81_SCGE_AB21.2x36mers.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 B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.1x36mers.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 B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.2x36mers.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 B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.2x36mers.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 B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.1x36mers.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 B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.2x36mers.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 B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B058_180718L20_exp180227_MS63_SCGE-00nM-BE_AB21.2x36mers.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 B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.1x36mers.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 B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.2x36mers.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 B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.2x36mers.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 B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.1x36mers.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 B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.2x36mers.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 B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B059_180718L25_exp180227_MS63_SCGE-10nM-BE_AB21.2x36mers.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 B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.1x36mers.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 B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.2x36mers.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 B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.2x36mers.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 B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.1x36mers.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 B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.2x36mers.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 B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B060_180718L30_exp180227_MS63_SCGE-30nM-BE_AB21.2x36mers.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 B061_180731L01_exp180711_MS01_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B061_180731L01_exp180711_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 B061_180731L01_exp180711_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B061_180731L01_exp180711_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 B061_180731L01_exp180711_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B061_180731L01_exp180711_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 B061_180731L01_exp180711_MS01_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B061_180731L01_exp180711_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 B061_180731L01_exp180711_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B061_180731L01_exp180711_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 B061_180731L01_exp180711_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B061_180731L01_exp180711_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 B062_180731L13_exp180711_MS80_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B062_180731L13_exp180711_MS80_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 B062_180731L13_exp180711_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B062_180731L13_exp180711_MS80_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 B062_180731L13_exp180711_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B062_180731L13_exp180711_MS80_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 B062_180731L13_exp180711_MS80_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B062_180731L13_exp180711_MS80_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 B062_180731L13_exp180711_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B062_180731L13_exp180711_MS80_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 B062_180731L13_exp180711_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B062_180731L13_exp180711_MS80_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 B063_180731L25_exp180711_MS81_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B063_180731L25_exp180711_MS81_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 B063_180731L25_exp180711_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B063_180731L25_exp180711_MS81_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 B063_180731L25_exp180711_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B063_180731L25_exp180711_MS81_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 B063_180731L25_exp180711_MS81_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B063_180731L25_exp180711_MS81_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 B063_180731L25_exp180711_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B063_180731L25_exp180711_MS81_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 B063_180731L25_exp180711_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B063_180731L25_exp180711_MS81_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 B064_180723L01_exp180712_MS63_SCGE-00nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B064_180723L01_exp180712_MS63_SCGE-00nM-BE_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 B064_180723L01_exp180712_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B064_180723L01_exp180712_MS63_SCGE-00nM-BE_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 B064_180723L01_exp180712_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B064_180723L01_exp180712_MS63_SCGE-00nM-BE_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 B064_180723L01_exp180712_MS63_SCGE-00nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B064_180723L01_exp180712_MS63_SCGE-00nM-BE_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 B064_180723L01_exp180712_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B064_180723L01_exp180712_MS63_SCGE-00nM-BE_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 B064_180723L01_exp180712_MS63_SCGE-00nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B064_180723L01_exp180712_MS63_SCGE-00nM-BE_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 B065_180723L07_exp180712_MS63_SCGE-10nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B065_180723L07_exp180712_MS63_SCGE-10nM-BE_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 B065_180723L07_exp180712_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B065_180723L07_exp180712_MS63_SCGE-10nM-BE_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 B065_180723L07_exp180712_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B065_180723L07_exp180712_MS63_SCGE-10nM-BE_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 B065_180723L07_exp180712_MS63_SCGE-10nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B065_180723L07_exp180712_MS63_SCGE-10nM-BE_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 B065_180723L07_exp180712_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B065_180723L07_exp180712_MS63_SCGE-10nM-BE_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 B065_180723L07_exp180712_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B065_180723L07_exp180712_MS63_SCGE-10nM-BE_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 B066_180723L13_exp180712_MS63_SCGE-30nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B066_180723L13_exp180712_MS63_SCGE-30nM-BE_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 B066_180723L13_exp180712_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B066_180723L13_exp180712_MS63_SCGE-30nM-BE_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 B066_180723L13_exp180712_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B066_180723L13_exp180712_MS63_SCGE-30nM-BE_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 B066_180723L13_exp180712_MS63_SCGE-30nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B066_180723L13_exp180712_MS63_SCGE-30nM-BE_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 B066_180723L13_exp180712_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B066_180723L13_exp180712_MS63_SCGE-30nM-BE_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 B066_180723L13_exp180712_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B066_180723L13_exp180712_MS63_SCGE-30nM-BE_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 B067_180731L02_exp180711_MS01_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B067_180731L02_exp180711_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 B067_180731L02_exp180711_MS01_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B067_180731L02_exp180711_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 B067_180731L02_exp180711_MS01_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B067_180731L02_exp180711_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 B067_180731L02_exp180711_MS01_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B067_180731L02_exp180711_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 B067_180731L02_exp180711_MS01_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B067_180731L02_exp180711_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 B067_180731L02_exp180711_MS01_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B067_180731L02_exp180711_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 B068_180731L14_exp180711_MS80_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B068_180731L14_exp180711_MS80_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 B068_180731L14_exp180711_MS80_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B068_180731L14_exp180711_MS80_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 B068_180731L14_exp180711_MS80_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B068_180731L14_exp180711_MS80_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 B068_180731L14_exp180711_MS80_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B068_180731L14_exp180711_MS80_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 B068_180731L14_exp180711_MS80_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B068_180731L14_exp180711_MS80_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 B068_180731L14_exp180711_MS80_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B068_180731L14_exp180711_MS80_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 B069_180731L26_exp180711_MS81_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B069_180731L26_exp180711_MS81_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 B069_180731L26_exp180711_MS81_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B069_180731L26_exp180711_MS81_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 B069_180731L26_exp180711_MS81_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B069_180731L26_exp180711_MS81_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 B069_180731L26_exp180711_MS81_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B069_180731L26_exp180711_MS81_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 B069_180731L26_exp180711_MS81_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B069_180731L26_exp180711_MS81_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 B069_180731L26_exp180711_MS81_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B069_180731L26_exp180711_MS81_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 B070_180723L02_exp180712_MS63_SCGE-00nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B070_180723L02_exp180712_MS63_SCGE-00nM-BE_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 B070_180723L02_exp180712_MS63_SCGE-00nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B070_180723L02_exp180712_MS63_SCGE-00nM-BE_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 B070_180723L02_exp180712_MS63_SCGE-00nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B070_180723L02_exp180712_MS63_SCGE-00nM-BE_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 B070_180723L02_exp180712_MS63_SCGE-00nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B070_180723L02_exp180712_MS63_SCGE-00nM-BE_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 B070_180723L02_exp180712_MS63_SCGE-00nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B070_180723L02_exp180712_MS63_SCGE-00nM-BE_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 B070_180723L02_exp180712_MS63_SCGE-00nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B070_180723L02_exp180712_MS63_SCGE-00nM-BE_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 B071_180723L08_exp180712_MS63_SCGE-10nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B071_180723L08_exp180712_MS63_SCGE-10nM-BE_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 B071_180723L08_exp180712_MS63_SCGE-10nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B071_180723L08_exp180712_MS63_SCGE-10nM-BE_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 B071_180723L08_exp180712_MS63_SCGE-10nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B071_180723L08_exp180712_MS63_SCGE-10nM-BE_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 B071_180723L08_exp180712_MS63_SCGE-10nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B071_180723L08_exp180712_MS63_SCGE-10nM-BE_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 B071_180723L08_exp180712_MS63_SCGE-10nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B071_180723L08_exp180712_MS63_SCGE-10nM-BE_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 B071_180723L08_exp180712_MS63_SCGE-10nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B071_180723L08_exp180712_MS63_SCGE-10nM-BE_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 B072_180723L14_exp180712_MS63_SCGE-30nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B072_180723L14_exp180712_MS63_SCGE-30nM-BE_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 B072_180723L14_exp180712_MS63_SCGE-30nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B072_180723L14_exp180712_MS63_SCGE-30nM-BE_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 B072_180723L14_exp180712_MS63_SCGE-30nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B072_180723L14_exp180712_MS63_SCGE-30nM-BE_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 B072_180723L14_exp180712_MS63_SCGE-30nM-BE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B072_180723L14_exp180712_MS63_SCGE-30nM-BE_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 B072_180723L14_exp180712_MS63_SCGE-30nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B072_180723L14_exp180712_MS63_SCGE-30nM-BE_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 B072_180723L14_exp180712_MS63_SCGE-30nM-BE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B072_180723L14_exp180712_MS63_SCGE-30nM-BE_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 B073_180731L03_exp180711_MS01_SCGE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B073_180731L03_exp180711_MS01_SCGE_AB04.1x36mers.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 B073_180731L03_exp180711_MS01_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B073_180731L03_exp180711_MS01_SCGE_AB04.2x36mers.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 B073_180731L03_exp180711_MS01_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B073_180731L03_exp180711_MS01_SCGE_AB04.2x36mers.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 B073_180731L03_exp180711_MS01_SCGE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B073_180731L03_exp180711_MS01_SCGE_AB04.1x36mers.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 B073_180731L03_exp180711_MS01_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B073_180731L03_exp180711_MS01_SCGE_AB04.2x36mers.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 B073_180731L03_exp180711_MS01_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B073_180731L03_exp180711_MS01_SCGE_AB04.2x36mers.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 B074_180731L15_exp180711_MS80_SCGE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B074_180731L15_exp180711_MS80_SCGE_AB04.1x36mers.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 B074_180731L15_exp180711_MS80_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B074_180731L15_exp180711_MS80_SCGE_AB04.2x36mers.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 B074_180731L15_exp180711_MS80_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B074_180731L15_exp180711_MS80_SCGE_AB04.2x36mers.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 B074_180731L15_exp180711_MS80_SCGE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B074_180731L15_exp180711_MS80_SCGE_AB04.1x36mers.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 B074_180731L15_exp180711_MS80_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B074_180731L15_exp180711_MS80_SCGE_AB04.2x36mers.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 B074_180731L15_exp180711_MS80_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B074_180731L15_exp180711_MS80_SCGE_AB04.2x36mers.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 B075_180731L27_exp180711_MS81_SCGE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B075_180731L27_exp180711_MS81_SCGE_AB04.1x36mers.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 B075_180731L27_exp180711_MS81_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B075_180731L27_exp180711_MS81_SCGE_AB04.2x36mers.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 B075_180731L27_exp180711_MS81_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B075_180731L27_exp180711_MS81_SCGE_AB04.2x36mers.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 B075_180731L27_exp180711_MS81_SCGE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B075_180731L27_exp180711_MS81_SCGE_AB04.1x36mers.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 B075_180731L27_exp180711_MS81_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B075_180731L27_exp180711_MS81_SCGE_AB04.2x36mers.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 B075_180731L27_exp180711_MS81_SCGE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B075_180731L27_exp180711_MS81_SCGE_AB04.2x36mers.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 B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.1x36mers.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 B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.2x36mers.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 B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.2x36mers.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 B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.1x36mers.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 B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.2x36mers.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 B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B076_180723L03_exp180712_MS63_SCGE-00nM-BE_AB04.2x36mers.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 B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.1x36mers.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 B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.2x36mers.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 B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.2x36mers.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 B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.1x36mers.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 B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.2x36mers.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 B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B077_180723L09_exp180712_MS63_SCGE-10nM-BE_AB04.2x36mers.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 B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.1x36mers.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 B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.2x36mers.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 B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.2x36mers.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 B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.1x36mers.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 B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.2x36mers.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 B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B078_180723L15_exp180712_MS63_SCGE-30nM-BE_AB04.2x36mers.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 B079_180731L04_exp180711_MS01_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B079_180731L04_exp180711_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 B079_180731L04_exp180711_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B079_180731L04_exp180711_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 B079_180731L04_exp180711_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B079_180731L04_exp180711_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 B079_180731L04_exp180711_MS01_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B079_180731L04_exp180711_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 B079_180731L04_exp180711_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B079_180731L04_exp180711_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 B079_180731L04_exp180711_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B079_180731L04_exp180711_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 B080_180731L10_exp180711_MS81_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B080_180731L10_exp180711_MS81_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 B080_180731L10_exp180711_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B080_180731L10_exp180711_MS81_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 B080_180731L10_exp180711_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B080_180731L10_exp180711_MS81_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 B080_180731L10_exp180711_MS81_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B080_180731L10_exp180711_MS81_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 B080_180731L10_exp180711_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B080_180731L10_exp180711_MS81_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 B080_180731L10_exp180711_MS81_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B080_180731L10_exp180711_MS81_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 B081_180731L16_exp180711_MS80_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B081_180731L16_exp180711_MS80_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 B081_180731L16_exp180711_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B081_180731L16_exp180711_MS80_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 B081_180731L16_exp180711_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B081_180731L16_exp180711_MS80_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 B081_180731L16_exp180711_MS80_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B081_180731L16_exp180711_MS80_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 B081_180731L16_exp180711_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B081_180731L16_exp180711_MS80_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 B081_180731L16_exp180711_MS80_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B081_180731L16_exp180711_MS80_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 B082_180723L04_exp180712_MS63_SCGE-00nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B082_180723L04_exp180712_MS63_SCGE-00nM-BE_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 B082_180723L04_exp180712_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B082_180723L04_exp180712_MS63_SCGE-00nM-BE_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 B082_180723L04_exp180712_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B082_180723L04_exp180712_MS63_SCGE-00nM-BE_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 B082_180723L04_exp180712_MS63_SCGE-00nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B082_180723L04_exp180712_MS63_SCGE-00nM-BE_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 B082_180723L04_exp180712_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B082_180723L04_exp180712_MS63_SCGE-00nM-BE_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 B082_180723L04_exp180712_MS63_SCGE-00nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B082_180723L04_exp180712_MS63_SCGE-00nM-BE_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 B083_180723L10_exp180712_MS63_SCGE-10nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B083_180723L10_exp180712_MS63_SCGE-10nM-BE_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 B083_180723L10_exp180712_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B083_180723L10_exp180712_MS63_SCGE-10nM-BE_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 B083_180723L10_exp180712_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B083_180723L10_exp180712_MS63_SCGE-10nM-BE_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 B083_180723L10_exp180712_MS63_SCGE-10nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B083_180723L10_exp180712_MS63_SCGE-10nM-BE_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 B083_180723L10_exp180712_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B083_180723L10_exp180712_MS63_SCGE-10nM-BE_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 B083_180723L10_exp180712_MS63_SCGE-10nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B083_180723L10_exp180712_MS63_SCGE-10nM-BE_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 B084_180723L16_exp180712_MS63_SCGE-30nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B084_180723L16_exp180712_MS63_SCGE-30nM-BE_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 B084_180723L16_exp180712_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B084_180723L16_exp180712_MS63_SCGE-30nM-BE_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 B084_180723L16_exp180712_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B084_180723L16_exp180712_MS63_SCGE-30nM-BE_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 B084_180723L16_exp180712_MS63_SCGE-30nM-BE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B084_180723L16_exp180712_MS63_SCGE-30nM-BE_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 B084_180723L16_exp180712_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B084_180723L16_exp180712_MS63_SCGE-30nM-BE_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 B084_180723L16_exp180712_MS63_SCGE-30nM-BE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B084_180723L16_exp180712_MS63_SCGE-30nM-BE_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 B085_180731L05_exp180711_MS01_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B085_180731L05_exp180711_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 B085_180731L05_exp180711_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B085_180731L05_exp180711_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 B085_180731L05_exp180711_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B085_180731L05_exp180711_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 B085_180731L05_exp180711_MS01_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B085_180731L05_exp180711_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 B085_180731L05_exp180711_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B085_180731L05_exp180711_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 B085_180731L05_exp180711_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B085_180731L05_exp180711_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B086_180731L17_exp180711_MS80_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B086_180731L17_exp180711_MS80_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 B086_180731L17_exp180711_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B086_180731L17_exp180711_MS80_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 B086_180731L17_exp180711_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B086_180731L17_exp180711_MS80_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 B086_180731L17_exp180711_MS80_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B086_180731L17_exp180711_MS80_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 B086_180731L17_exp180711_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B086_180731L17_exp180711_MS80_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 B086_180731L17_exp180711_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B086_180731L17_exp180711_MS80_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B087_180731L29_exp180711_MS81_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B087_180731L29_exp180711_MS81_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 B087_180731L29_exp180711_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B087_180731L29_exp180711_MS81_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 B087_180731L29_exp180711_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B087_180731L29_exp180711_MS81_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 B087_180731L29_exp180711_MS81_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B087_180731L29_exp180711_MS81_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 B087_180731L29_exp180711_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B087_180731L29_exp180711_MS81_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 B087_180731L29_exp180711_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B087_180731L29_exp180711_MS81_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B088_180723L05_exp180712_MS63_SCGE-00nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B088_180723L05_exp180712_MS63_SCGE-00nM-BE_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 B088_180723L05_exp180712_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B088_180723L05_exp180712_MS63_SCGE-00nM-BE_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 B088_180723L05_exp180712_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B088_180723L05_exp180712_MS63_SCGE-00nM-BE_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 B088_180723L05_exp180712_MS63_SCGE-00nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B088_180723L05_exp180712_MS63_SCGE-00nM-BE_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 B088_180723L05_exp180712_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B088_180723L05_exp180712_MS63_SCGE-00nM-BE_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 B088_180723L05_exp180712_MS63_SCGE-00nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B088_180723L05_exp180712_MS63_SCGE-00nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B089_180723L11_exp180712_MS63_SCGE-10nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B089_180723L11_exp180712_MS63_SCGE-10nM-BE_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 B089_180723L11_exp180712_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B089_180723L11_exp180712_MS63_SCGE-10nM-BE_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 B089_180723L11_exp180712_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B089_180723L11_exp180712_MS63_SCGE-10nM-BE_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 B089_180723L11_exp180712_MS63_SCGE-10nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B089_180723L11_exp180712_MS63_SCGE-10nM-BE_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 B089_180723L11_exp180712_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B089_180723L11_exp180712_MS63_SCGE-10nM-BE_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 B089_180723L11_exp180712_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B089_180723L11_exp180712_MS63_SCGE-10nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B090_180723L17_exp180712_MS63_SCGE-30nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B090_180723L17_exp180712_MS63_SCGE-30nM-BE_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 B090_180723L17_exp180712_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B090_180723L17_exp180712_MS63_SCGE-30nM-BE_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 B090_180723L17_exp180712_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B090_180723L17_exp180712_MS63_SCGE-30nM-BE_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 B090_180723L17_exp180712_MS63_SCGE-30nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B090_180723L17_exp180712_MS63_SCGE-30nM-BE_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 B090_180723L17_exp180712_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B090_180723L17_exp180712_MS63_SCGE-30nM-BE_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 B090_180723L17_exp180712_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B090_180723L17_exp180712_MS63_SCGE-30nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.1x36mers.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 B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.2x36mers.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 B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.2x36mers.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 B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.1x36mers.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 B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.2x36mers.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 B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B091_180723L06_exp180712_MS63_SCGE-00nM-BE_AB21.2x36mers.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 B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.1x36mers.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 B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.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 B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.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 B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.1x36mers.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 B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.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 B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B092_180723L12_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.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 B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.1x36mers.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 B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.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 B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.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 B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.1x36mers.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 B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.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 B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B093_180723L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.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 B094_180731L06_exp180711_MS01_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B094_180731L06_exp180711_MS01_SCGE_AB21.1x36mers.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 B094_180731L06_exp180711_MS01_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B094_180731L06_exp180711_MS01_SCGE_AB21.2x36mers.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 B094_180731L06_exp180711_MS01_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B094_180731L06_exp180711_MS01_SCGE_AB21.2x36mers.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 B094_180731L06_exp180711_MS01_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B094_180731L06_exp180711_MS01_SCGE_AB21.1x36mers.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 B094_180731L06_exp180711_MS01_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B094_180731L06_exp180711_MS01_SCGE_AB21.2x36mers.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 B094_180731L06_exp180711_MS01_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B094_180731L06_exp180711_MS01_SCGE_AB21.2x36mers.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 B095_180731L18_exp180711_MS80_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B095_180731L18_exp180711_MS80_SCGE_AB21.1x36mers.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 B095_180731L18_exp180711_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B095_180731L18_exp180711_MS80_SCGE_AB21.2x36mers.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 B095_180731L18_exp180711_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B095_180731L18_exp180711_MS80_SCGE_AB21.2x36mers.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 B095_180731L18_exp180711_MS80_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B095_180731L18_exp180711_MS80_SCGE_AB21.1x36mers.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 B095_180731L18_exp180711_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B095_180731L18_exp180711_MS80_SCGE_AB21.2x36mers.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 B095_180731L18_exp180711_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B095_180731L18_exp180711_MS80_SCGE_AB21.2x36mers.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 B096_180731L30_exp180711_MS81_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B096_180731L30_exp180711_MS81_SCGE_AB21.1x36mers.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 B096_180731L30_exp180711_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B096_180731L30_exp180711_MS81_SCGE_AB21.2x36mers.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 B096_180731L30_exp180711_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B096_180731L30_exp180711_MS81_SCGE_AB21.2x36mers.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 B096_180731L30_exp180711_MS81_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-B096_180731L30_exp180711_MS81_SCGE_AB21.1x36mers.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 B096_180731L30_exp180711_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B096_180731L30_exp180711_MS81_SCGE_AB21.2x36mers.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 B096_180731L30_exp180711_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-B096_180731L30_exp180711_MS81_SCGE_AB21.2x36mers.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 C001_180731L37_exp180709_MS55_SCGE_Fr1_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C001_180731L37_exp180709_MS55_SCGE_Fr1_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 C001_180731L37_exp180709_MS55_SCGE_Fr1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C001_180731L37_exp180709_MS55_SCGE_Fr1_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 C001_180731L37_exp180709_MS55_SCGE_Fr1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C001_180731L37_exp180709_MS55_SCGE_Fr1_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 C001_180731L37_exp180709_MS55_SCGE_Fr1_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C001_180731L37_exp180709_MS55_SCGE_Fr1_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 C001_180731L37_exp180709_MS55_SCGE_Fr1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C001_180731L37_exp180709_MS55_SCGE_Fr1_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 C001_180731L37_exp180709_MS55_SCGE_Fr1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C001_180731L37_exp180709_MS55_SCGE_Fr1_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 C002_180731L07_exp180709_MS55_SCGE_Fr2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C002_180731L07_exp180709_MS55_SCGE_Fr2_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 C002_180731L07_exp180709_MS55_SCGE_Fr2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C002_180731L07_exp180709_MS55_SCGE_Fr2_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 C002_180731L07_exp180709_MS55_SCGE_Fr2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C002_180731L07_exp180709_MS55_SCGE_Fr2_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 C002_180731L07_exp180709_MS55_SCGE_Fr2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C002_180731L07_exp180709_MS55_SCGE_Fr2_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 C002_180731L07_exp180709_MS55_SCGE_Fr2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C002_180731L07_exp180709_MS55_SCGE_Fr2_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 C002_180731L07_exp180709_MS55_SCGE_Fr2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C002_180731L07_exp180709_MS55_SCGE_Fr2_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 C003_180731L19_exp180709_MS55_SCGE_Fr3_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C003_180731L19_exp180709_MS55_SCGE_Fr3_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 C003_180731L19_exp180709_MS55_SCGE_Fr3_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C003_180731L19_exp180709_MS55_SCGE_Fr3_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 C003_180731L19_exp180709_MS55_SCGE_Fr3_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C003_180731L19_exp180709_MS55_SCGE_Fr3_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 C003_180731L19_exp180709_MS55_SCGE_Fr3_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C003_180731L19_exp180709_MS55_SCGE_Fr3_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 C003_180731L19_exp180709_MS55_SCGE_Fr3_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C003_180731L19_exp180709_MS55_SCGE_Fr3_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 C003_180731L19_exp180709_MS55_SCGE_Fr3_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C003_180731L19_exp180709_MS55_SCGE_Fr3_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 C004_180731L31_exp180709_MS55_SCGE_Fr4_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C004_180731L31_exp180709_MS55_SCGE_Fr4_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 C004_180731L31_exp180709_MS55_SCGE_Fr4_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C004_180731L31_exp180709_MS55_SCGE_Fr4_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 C004_180731L31_exp180709_MS55_SCGE_Fr4_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C004_180731L31_exp180709_MS55_SCGE_Fr4_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 C004_180731L31_exp180709_MS55_SCGE_Fr4_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C004_180731L31_exp180709_MS55_SCGE_Fr4_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 C004_180731L31_exp180709_MS55_SCGE_Fr4_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C004_180731L31_exp180709_MS55_SCGE_Fr4_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 C004_180731L31_exp180709_MS55_SCGE_Fr4_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C004_180731L31_exp180709_MS55_SCGE_Fr4_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 C005_180731L38_exp180709_MS55_SCGE_Fr1_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C005_180731L38_exp180709_MS55_SCGE_Fr1_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 C005_180731L38_exp180709_MS55_SCGE_Fr1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C005_180731L38_exp180709_MS55_SCGE_Fr1_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 C005_180731L38_exp180709_MS55_SCGE_Fr1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C005_180731L38_exp180709_MS55_SCGE_Fr1_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 C005_180731L38_exp180709_MS55_SCGE_Fr1_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C005_180731L38_exp180709_MS55_SCGE_Fr1_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 C005_180731L38_exp180709_MS55_SCGE_Fr1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C005_180731L38_exp180709_MS55_SCGE_Fr1_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 C005_180731L38_exp180709_MS55_SCGE_Fr1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C005_180731L38_exp180709_MS55_SCGE_Fr1_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 C006_180731L08_exp180709_MS55_SCGE_Fr2_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C006_180731L08_exp180709_MS55_SCGE_Fr2_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 C006_180731L08_exp180709_MS55_SCGE_Fr2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C006_180731L08_exp180709_MS55_SCGE_Fr2_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 C006_180731L08_exp180709_MS55_SCGE_Fr2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C006_180731L08_exp180709_MS55_SCGE_Fr2_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 C006_180731L08_exp180709_MS55_SCGE_Fr2_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C006_180731L08_exp180709_MS55_SCGE_Fr2_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 C006_180731L08_exp180709_MS55_SCGE_Fr2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C006_180731L08_exp180709_MS55_SCGE_Fr2_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 C006_180731L08_exp180709_MS55_SCGE_Fr2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C006_180731L08_exp180709_MS55_SCGE_Fr2_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 C007_180731L20_exp180709_MS55_SCGE_Fr3_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C007_180731L20_exp180709_MS55_SCGE_Fr3_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 C007_180731L20_exp180709_MS55_SCGE_Fr3_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C007_180731L20_exp180709_MS55_SCGE_Fr3_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 C007_180731L20_exp180709_MS55_SCGE_Fr3_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C007_180731L20_exp180709_MS55_SCGE_Fr3_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 C007_180731L20_exp180709_MS55_SCGE_Fr3_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C007_180731L20_exp180709_MS55_SCGE_Fr3_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 C007_180731L20_exp180709_MS55_SCGE_Fr3_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C007_180731L20_exp180709_MS55_SCGE_Fr3_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 C007_180731L20_exp180709_MS55_SCGE_Fr3_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C007_180731L20_exp180709_MS55_SCGE_Fr3_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 C008_180731L32_exp180709_MS55_SCGE_Fr4_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C008_180731L32_exp180709_MS55_SCGE_Fr4_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 C008_180731L32_exp180709_MS55_SCGE_Fr4_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C008_180731L32_exp180709_MS55_SCGE_Fr4_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 C008_180731L32_exp180709_MS55_SCGE_Fr4_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C008_180731L32_exp180709_MS55_SCGE_Fr4_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 C008_180731L32_exp180709_MS55_SCGE_Fr4_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C008_180731L32_exp180709_MS55_SCGE_Fr4_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 C008_180731L32_exp180709_MS55_SCGE_Fr4_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C008_180731L32_exp180709_MS55_SCGE_Fr4_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 C008_180731L32_exp180709_MS55_SCGE_Fr4_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C008_180731L32_exp180709_MS55_SCGE_Fr4_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 C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.1x36mers.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 C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.2x36mers.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 C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.2x36mers.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 C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.1x36mers.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 C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.2x36mers.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 C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C009_180731L39_exp180709_MS55_SCGE_Fr1_AB04.2x36mers.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 C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.1x36mers.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 C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.2x36mers.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 C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.2x36mers.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 C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.1x36mers.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 C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.2x36mers.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 C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C010_180731L09_exp180709_MS55_SCGE_Fr2_AB04.2x36mers.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 C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.1x36mers.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 C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.2x36mers.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 C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.2x36mers.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 C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.1x36mers.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 C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.2x36mers.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 C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C011_180731L21_exp180709_MS55_SCGE_Fr3_AB04.2x36mers.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 C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.1x36mers.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 C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.2x36mers.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 C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.2x36mers.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 C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.1x36mers.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 C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.2x36mers.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 C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C012_180731L33_exp180709_MS55_SCGE_Fr4_AB04.2x36mers.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 C013_180731L22_exp180709_MS55_SCGE_Fr1_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C013_180731L22_exp180709_MS55_SCGE_Fr1_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 C013_180731L22_exp180709_MS55_SCGE_Fr1_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C013_180731L22_exp180709_MS55_SCGE_Fr1_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 C013_180731L22_exp180709_MS55_SCGE_Fr1_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C013_180731L22_exp180709_MS55_SCGE_Fr1_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 C013_180731L22_exp180709_MS55_SCGE_Fr1_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C013_180731L22_exp180709_MS55_SCGE_Fr1_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 C013_180731L22_exp180709_MS55_SCGE_Fr1_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C013_180731L22_exp180709_MS55_SCGE_Fr1_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 C013_180731L22_exp180709_MS55_SCGE_Fr1_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C013_180731L22_exp180709_MS55_SCGE_Fr1_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 C014_180731L28_exp180709_MS55_SCGE_Fr2_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C014_180731L28_exp180709_MS55_SCGE_Fr2_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 C014_180731L28_exp180709_MS55_SCGE_Fr2_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C014_180731L28_exp180709_MS55_SCGE_Fr2_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 C014_180731L28_exp180709_MS55_SCGE_Fr2_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C014_180731L28_exp180709_MS55_SCGE_Fr2_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 C014_180731L28_exp180709_MS55_SCGE_Fr2_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C014_180731L28_exp180709_MS55_SCGE_Fr2_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 C014_180731L28_exp180709_MS55_SCGE_Fr2_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C014_180731L28_exp180709_MS55_SCGE_Fr2_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 C014_180731L28_exp180709_MS55_SCGE_Fr2_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C014_180731L28_exp180709_MS55_SCGE_Fr2_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 C015_180731L34_exp180709_MS55_SCGE_Fr3_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C015_180731L34_exp180709_MS55_SCGE_Fr3_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 C015_180731L34_exp180709_MS55_SCGE_Fr3_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C015_180731L34_exp180709_MS55_SCGE_Fr3_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 C015_180731L34_exp180709_MS55_SCGE_Fr3_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C015_180731L34_exp180709_MS55_SCGE_Fr3_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 C015_180731L34_exp180709_MS55_SCGE_Fr3_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C015_180731L34_exp180709_MS55_SCGE_Fr3_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 C015_180731L34_exp180709_MS55_SCGE_Fr3_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C015_180731L34_exp180709_MS55_SCGE_Fr3_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 C015_180731L34_exp180709_MS55_SCGE_Fr3_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C015_180731L34_exp180709_MS55_SCGE_Fr3_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 C016_180731L40_exp180709_MS55_SCGE_Fr4_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C016_180731L40_exp180709_MS55_SCGE_Fr4_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 C016_180731L40_exp180709_MS55_SCGE_Fr4_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C016_180731L40_exp180709_MS55_SCGE_Fr4_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 C016_180731L40_exp180709_MS55_SCGE_Fr4_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C016_180731L40_exp180709_MS55_SCGE_Fr4_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 C016_180731L40_exp180709_MS55_SCGE_Fr4_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C016_180731L40_exp180709_MS55_SCGE_Fr4_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 C016_180731L40_exp180709_MS55_SCGE_Fr4_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C016_180731L40_exp180709_MS55_SCGE_Fr4_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 C016_180731L40_exp180709_MS55_SCGE_Fr4_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C016_180731L40_exp180709_MS55_SCGE_Fr4_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 C017_180731L41_exp180709_MS55_SCGE_Fr1_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C017_180731L41_exp180709_MS55_SCGE_Fr1_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 C017_180731L41_exp180709_MS55_SCGE_Fr1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C017_180731L41_exp180709_MS55_SCGE_Fr1_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 C017_180731L41_exp180709_MS55_SCGE_Fr1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C017_180731L41_exp180709_MS55_SCGE_Fr1_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 C017_180731L41_exp180709_MS55_SCGE_Fr1_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C017_180731L41_exp180709_MS55_SCGE_Fr1_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 C017_180731L41_exp180709_MS55_SCGE_Fr1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C017_180731L41_exp180709_MS55_SCGE_Fr1_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 C017_180731L41_exp180709_MS55_SCGE_Fr1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C017_180731L41_exp180709_MS55_SCGE_Fr1_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C018_180731L11_exp180709_MS55_SCGE_Fr2_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C018_180731L11_exp180709_MS55_SCGE_Fr2_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 C018_180731L11_exp180709_MS55_SCGE_Fr2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C018_180731L11_exp180709_MS55_SCGE_Fr2_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 C018_180731L11_exp180709_MS55_SCGE_Fr2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C018_180731L11_exp180709_MS55_SCGE_Fr2_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 C018_180731L11_exp180709_MS55_SCGE_Fr2_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C018_180731L11_exp180709_MS55_SCGE_Fr2_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 C018_180731L11_exp180709_MS55_SCGE_Fr2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C018_180731L11_exp180709_MS55_SCGE_Fr2_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 C018_180731L11_exp180709_MS55_SCGE_Fr2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C018_180731L11_exp180709_MS55_SCGE_Fr2_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C019_180731L23_exp180709_MS55_SCGE_Fr3_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C019_180731L23_exp180709_MS55_SCGE_Fr3_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 C019_180731L23_exp180709_MS55_SCGE_Fr3_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C019_180731L23_exp180709_MS55_SCGE_Fr3_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 C019_180731L23_exp180709_MS55_SCGE_Fr3_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C019_180731L23_exp180709_MS55_SCGE_Fr3_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 C019_180731L23_exp180709_MS55_SCGE_Fr3_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C019_180731L23_exp180709_MS55_SCGE_Fr3_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 C019_180731L23_exp180709_MS55_SCGE_Fr3_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C019_180731L23_exp180709_MS55_SCGE_Fr3_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 C019_180731L23_exp180709_MS55_SCGE_Fr3_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C019_180731L23_exp180709_MS55_SCGE_Fr3_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C020_180731L35_exp180709_MS55_SCGE_Fr4_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C020_180731L35_exp180709_MS55_SCGE_Fr4_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 C020_180731L35_exp180709_MS55_SCGE_Fr4_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C020_180731L35_exp180709_MS55_SCGE_Fr4_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 C020_180731L35_exp180709_MS55_SCGE_Fr4_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C020_180731L35_exp180709_MS55_SCGE_Fr4_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 C020_180731L35_exp180709_MS55_SCGE_Fr4_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C020_180731L35_exp180709_MS55_SCGE_Fr4_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 C020_180731L35_exp180709_MS55_SCGE_Fr4_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C020_180731L35_exp180709_MS55_SCGE_Fr4_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 C020_180731L35_exp180709_MS55_SCGE_Fr4_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C020_180731L35_exp180709_MS55_SCGE_Fr4_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.1x36mers.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 C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.2x36mers.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 C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.2x36mers.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 C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.1x36mers.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 C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.2x36mers.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 C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C021_180731L42_exp180709_MS55_SCGE_Fr1_AB21.2x36mers.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 C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.1x36mers.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 C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.2x36mers.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 C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.2x36mers.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 C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.1x36mers.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 C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.2x36mers.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 C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C022_180731L12_exp180709_MS55_SCGE_Fr2_AB21.2x36mers.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 C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.1x36mers.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 C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.2x36mers.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 C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.2x36mers.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 C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.1x36mers.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 C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.2x36mers.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 C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C023_180731L24_exp180709_MS55_SCGE_Fr3_AB21.2x36mers.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 C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.1x36mers.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 C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.2x36mers.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 C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.2x36mers.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 C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.1x36mers.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 C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.2x36mers.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 C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C024_180731L36_exp180709_MS55_SCGE_Fr4_AB21.2x36mers.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 C025_200131L01_MS1_SCGE_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C025_200131L01_MS1_SCGE_FrA_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 C025_200131L01_MS1_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C025_200131L01_MS1_SCGE_FrA_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 C025_200131L01_MS1_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C025_200131L01_MS1_SCGE_FrA_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 C025_200131L01_MS1_SCGE_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C025_200131L01_MS1_SCGE_FrA_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 C025_200131L01_MS1_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C025_200131L01_MS1_SCGE_FrA_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 C025_200131L01_MS1_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C025_200131L01_MS1_SCGE_FrA_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 C026_200131L02_MS1_SCGE_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C026_200131L02_MS1_SCGE_FrB_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 C026_200131L02_MS1_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C026_200131L02_MS1_SCGE_FrB_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 C026_200131L02_MS1_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C026_200131L02_MS1_SCGE_FrB_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 C026_200131L02_MS1_SCGE_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C026_200131L02_MS1_SCGE_FrB_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 C026_200131L02_MS1_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C026_200131L02_MS1_SCGE_FrB_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 C026_200131L02_MS1_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C026_200131L02_MS1_SCGE_FrB_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 C027_200131L03_MS1_SCGE_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C027_200131L03_MS1_SCGE_FrC_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 C027_200131L03_MS1_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C027_200131L03_MS1_SCGE_FrC_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 C027_200131L03_MS1_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C027_200131L03_MS1_SCGE_FrC_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 C027_200131L03_MS1_SCGE_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C027_200131L03_MS1_SCGE_FrC_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 C027_200131L03_MS1_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C027_200131L03_MS1_SCGE_FrC_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 C027_200131L03_MS1_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C027_200131L03_MS1_SCGE_FrC_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 C028_200131L04_MS1_SCGE_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C028_200131L04_MS1_SCGE_FrD_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 C028_200131L04_MS1_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C028_200131L04_MS1_SCGE_FrD_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 C028_200131L04_MS1_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C028_200131L04_MS1_SCGE_FrD_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 C028_200131L04_MS1_SCGE_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C028_200131L04_MS1_SCGE_FrD_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 C028_200131L04_MS1_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C028_200131L04_MS1_SCGE_FrD_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 C028_200131L04_MS1_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C028_200131L04_MS1_SCGE_FrD_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 C029_200131L05_MS86_SCGE_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C029_200131L05_MS86_SCGE_FrA_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 C029_200131L05_MS86_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C029_200131L05_MS86_SCGE_FrA_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 C029_200131L05_MS86_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C029_200131L05_MS86_SCGE_FrA_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 C029_200131L05_MS86_SCGE_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C029_200131L05_MS86_SCGE_FrA_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 C029_200131L05_MS86_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C029_200131L05_MS86_SCGE_FrA_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 C029_200131L05_MS86_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C029_200131L05_MS86_SCGE_FrA_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 C030_200131L06_MS86_SCGE_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C030_200131L06_MS86_SCGE_FrB_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 C030_200131L06_MS86_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C030_200131L06_MS86_SCGE_FrB_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 C030_200131L06_MS86_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C030_200131L06_MS86_SCGE_FrB_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 C030_200131L06_MS86_SCGE_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C030_200131L06_MS86_SCGE_FrB_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 C030_200131L06_MS86_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C030_200131L06_MS86_SCGE_FrB_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 C030_200131L06_MS86_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C030_200131L06_MS86_SCGE_FrB_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 C031_200131L07_MS86_SCGE_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C031_200131L07_MS86_SCGE_FrC_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 C031_200131L07_MS86_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C031_200131L07_MS86_SCGE_FrC_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 C031_200131L07_MS86_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C031_200131L07_MS86_SCGE_FrC_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 C031_200131L07_MS86_SCGE_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C031_200131L07_MS86_SCGE_FrC_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 C031_200131L07_MS86_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C031_200131L07_MS86_SCGE_FrC_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 C031_200131L07_MS86_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C031_200131L07_MS86_SCGE_FrC_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 C032_200131L08_MS86_SCGE_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C032_200131L08_MS86_SCGE_FrD_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 C032_200131L08_MS86_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C032_200131L08_MS86_SCGE_FrD_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 C032_200131L08_MS86_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C032_200131L08_MS86_SCGE_FrD_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 C032_200131L08_MS86_SCGE_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C032_200131L08_MS86_SCGE_FrD_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 C032_200131L08_MS86_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C032_200131L08_MS86_SCGE_FrD_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 C032_200131L08_MS86_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C032_200131L08_MS86_SCGE_FrD_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 C033_200131L09_MS1_SCGE_FrA_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C033_200131L09_MS1_SCGE_FrA_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 C033_200131L09_MS1_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C033_200131L09_MS1_SCGE_FrA_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 C033_200131L09_MS1_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C033_200131L09_MS1_SCGE_FrA_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 C033_200131L09_MS1_SCGE_FrA_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C033_200131L09_MS1_SCGE_FrA_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 C033_200131L09_MS1_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C033_200131L09_MS1_SCGE_FrA_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 C033_200131L09_MS1_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C033_200131L09_MS1_SCGE_FrA_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C034_200131L10_MS1_SCGE_FrB_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C034_200131L10_MS1_SCGE_FrB_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 C034_200131L10_MS1_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C034_200131L10_MS1_SCGE_FrB_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 C034_200131L10_MS1_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C034_200131L10_MS1_SCGE_FrB_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 C034_200131L10_MS1_SCGE_FrB_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C034_200131L10_MS1_SCGE_FrB_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 C034_200131L10_MS1_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C034_200131L10_MS1_SCGE_FrB_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 C034_200131L10_MS1_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C034_200131L10_MS1_SCGE_FrB_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C035_200131L11_MS1_SCGE_FrC_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C035_200131L11_MS1_SCGE_FrC_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 C035_200131L11_MS1_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C035_200131L11_MS1_SCGE_FrC_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 C035_200131L11_MS1_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C035_200131L11_MS1_SCGE_FrC_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 C035_200131L11_MS1_SCGE_FrC_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C035_200131L11_MS1_SCGE_FrC_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 C035_200131L11_MS1_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C035_200131L11_MS1_SCGE_FrC_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 C035_200131L11_MS1_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C035_200131L11_MS1_SCGE_FrC_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C036_200131L12_MS1_SCGE_FrD_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C036_200131L12_MS1_SCGE_FrD_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 C036_200131L12_MS1_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C036_200131L12_MS1_SCGE_FrD_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 C036_200131L12_MS1_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C036_200131L12_MS1_SCGE_FrD_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 C036_200131L12_MS1_SCGE_FrD_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C036_200131L12_MS1_SCGE_FrD_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 C036_200131L12_MS1_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C036_200131L12_MS1_SCGE_FrD_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 C036_200131L12_MS1_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C036_200131L12_MS1_SCGE_FrD_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C037_200131L13_MS86_SCGE_FrA_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C037_200131L13_MS86_SCGE_FrA_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 C037_200131L13_MS86_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C037_200131L13_MS86_SCGE_FrA_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 C037_200131L13_MS86_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C037_200131L13_MS86_SCGE_FrA_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 C037_200131L13_MS86_SCGE_FrA_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C037_200131L13_MS86_SCGE_FrA_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 C037_200131L13_MS86_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C037_200131L13_MS86_SCGE_FrA_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 C037_200131L13_MS86_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C037_200131L13_MS86_SCGE_FrA_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C038_200131L14_MS86_SCGE_FrB_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C038_200131L14_MS86_SCGE_FrB_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 C038_200131L14_MS86_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C038_200131L14_MS86_SCGE_FrB_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 C038_200131L14_MS86_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C038_200131L14_MS86_SCGE_FrB_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 C038_200131L14_MS86_SCGE_FrB_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C038_200131L14_MS86_SCGE_FrB_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 C038_200131L14_MS86_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C038_200131L14_MS86_SCGE_FrB_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 C038_200131L14_MS86_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C038_200131L14_MS86_SCGE_FrB_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C039_200131L15_MS86_SCGE_FrC_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C039_200131L15_MS86_SCGE_FrC_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 C039_200131L15_MS86_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C039_200131L15_MS86_SCGE_FrC_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 C039_200131L15_MS86_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C039_200131L15_MS86_SCGE_FrC_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 C039_200131L15_MS86_SCGE_FrC_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C039_200131L15_MS86_SCGE_FrC_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 C039_200131L15_MS86_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C039_200131L15_MS86_SCGE_FrC_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 C039_200131L15_MS86_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C039_200131L15_MS86_SCGE_FrC_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C040_200131L16_MS86_SCGE_FrD_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C040_200131L16_MS86_SCGE_FrD_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 C040_200131L16_MS86_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C040_200131L16_MS86_SCGE_FrD_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 C040_200131L16_MS86_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C040_200131L16_MS86_SCGE_FrD_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 C040_200131L16_MS86_SCGE_FrD_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C040_200131L16_MS86_SCGE_FrD_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 C040_200131L16_MS86_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C040_200131L16_MS86_SCGE_FrD_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 C040_200131L16_MS86_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C040_200131L16_MS86_SCGE_FrD_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C041_200131L17_MS1_SCGE_FrA_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C041_200131L17_MS1_SCGE_FrA_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 C041_200131L17_MS1_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C041_200131L17_MS1_SCGE_FrA_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 C041_200131L17_MS1_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C041_200131L17_MS1_SCGE_FrA_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 C041_200131L17_MS1_SCGE_FrA_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C041_200131L17_MS1_SCGE_FrA_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 C041_200131L17_MS1_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C041_200131L17_MS1_SCGE_FrA_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 C041_200131L17_MS1_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C041_200131L17_MS1_SCGE_FrA_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 C042_200131L18_MS1_SCGE_FrB_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C042_200131L18_MS1_SCGE_FrB_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 C042_200131L18_MS1_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C042_200131L18_MS1_SCGE_FrB_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 C042_200131L18_MS1_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C042_200131L18_MS1_SCGE_FrB_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 C042_200131L18_MS1_SCGE_FrB_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C042_200131L18_MS1_SCGE_FrB_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 C042_200131L18_MS1_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C042_200131L18_MS1_SCGE_FrB_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 C042_200131L18_MS1_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C042_200131L18_MS1_SCGE_FrB_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 C043_200131L19_MS1_SCGE_FrC_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C043_200131L19_MS1_SCGE_FrC_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 C043_200131L19_MS1_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C043_200131L19_MS1_SCGE_FrC_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 C043_200131L19_MS1_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C043_200131L19_MS1_SCGE_FrC_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 C043_200131L19_MS1_SCGE_FrC_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C043_200131L19_MS1_SCGE_FrC_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 C043_200131L19_MS1_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C043_200131L19_MS1_SCGE_FrC_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 C043_200131L19_MS1_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C043_200131L19_MS1_SCGE_FrC_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 C044_200131L20_MS1_SCGE_FrD_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C044_200131L20_MS1_SCGE_FrD_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 C044_200131L20_MS1_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C044_200131L20_MS1_SCGE_FrD_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 C044_200131L20_MS1_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C044_200131L20_MS1_SCGE_FrD_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 C044_200131L20_MS1_SCGE_FrD_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C044_200131L20_MS1_SCGE_FrD_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 C044_200131L20_MS1_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C044_200131L20_MS1_SCGE_FrD_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 C044_200131L20_MS1_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C044_200131L20_MS1_SCGE_FrD_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 C045_200131L21_MS86_SCGE_FrA_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C045_200131L21_MS86_SCGE_FrA_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 C045_200131L21_MS86_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C045_200131L21_MS86_SCGE_FrA_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 C045_200131L21_MS86_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C045_200131L21_MS86_SCGE_FrA_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 C045_200131L21_MS86_SCGE_FrA_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C045_200131L21_MS86_SCGE_FrA_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 C045_200131L21_MS86_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C045_200131L21_MS86_SCGE_FrA_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 C045_200131L21_MS86_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C045_200131L21_MS86_SCGE_FrA_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 C046_200131L22_MS86_SCGE_FrB_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C046_200131L22_MS86_SCGE_FrB_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 C046_200131L22_MS86_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C046_200131L22_MS86_SCGE_FrB_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 C046_200131L22_MS86_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C046_200131L22_MS86_SCGE_FrB_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 C046_200131L22_MS86_SCGE_FrB_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C046_200131L22_MS86_SCGE_FrB_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 C046_200131L22_MS86_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C046_200131L22_MS86_SCGE_FrB_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 C046_200131L22_MS86_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C046_200131L22_MS86_SCGE_FrB_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 C047_200131L23_MS86_SCGE_FrC_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C047_200131L23_MS86_SCGE_FrC_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 C047_200131L23_MS86_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C047_200131L23_MS86_SCGE_FrC_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 C047_200131L23_MS86_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C047_200131L23_MS86_SCGE_FrC_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 C047_200131L23_MS86_SCGE_FrC_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C047_200131L23_MS86_SCGE_FrC_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 C047_200131L23_MS86_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C047_200131L23_MS86_SCGE_FrC_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 C047_200131L23_MS86_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C047_200131L23_MS86_SCGE_FrC_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 C048_200131L24_MS86_SCGE_FrD_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C048_200131L24_MS86_SCGE_FrD_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 C048_200131L24_MS86_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C048_200131L24_MS86_SCGE_FrD_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 C048_200131L24_MS86_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C048_200131L24_MS86_SCGE_FrD_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 C048_200131L24_MS86_SCGE_FrD_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C048_200131L24_MS86_SCGE_FrD_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 C048_200131L24_MS86_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C048_200131L24_MS86_SCGE_FrD_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 C048_200131L24_MS86_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C048_200131L24_MS86_SCGE_FrD_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 C049_200526L01_MS1_SCGE_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C049_200526L01_MS1_SCGE_FrA_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 C049_200526L01_MS1_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C049_200526L01_MS1_SCGE_FrA_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 C049_200526L01_MS1_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C049_200526L01_MS1_SCGE_FrA_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 C049_200526L01_MS1_SCGE_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C049_200526L01_MS1_SCGE_FrA_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 C049_200526L01_MS1_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C049_200526L01_MS1_SCGE_FrA_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 C049_200526L01_MS1_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C049_200526L01_MS1_SCGE_FrA_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 C050_200526L02_MS1_SCGE_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C050_200526L02_MS1_SCGE_FrB_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 C050_200526L02_MS1_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C050_200526L02_MS1_SCGE_FrB_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 C050_200526L02_MS1_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C050_200526L02_MS1_SCGE_FrB_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 C050_200526L02_MS1_SCGE_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C050_200526L02_MS1_SCGE_FrB_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 C050_200526L02_MS1_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C050_200526L02_MS1_SCGE_FrB_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 C050_200526L02_MS1_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C050_200526L02_MS1_SCGE_FrB_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 C051_200526L03_MS1_SCGE_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C051_200526L03_MS1_SCGE_FrC_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 C051_200526L03_MS1_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C051_200526L03_MS1_SCGE_FrC_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 C051_200526L03_MS1_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C051_200526L03_MS1_SCGE_FrC_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 C051_200526L03_MS1_SCGE_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C051_200526L03_MS1_SCGE_FrC_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 C051_200526L03_MS1_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C051_200526L03_MS1_SCGE_FrC_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 C051_200526L03_MS1_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C051_200526L03_MS1_SCGE_FrC_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 C052_200526L04_MS1_SCGE_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C052_200526L04_MS1_SCGE_FrD_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 C052_200526L04_MS1_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C052_200526L04_MS1_SCGE_FrD_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 C052_200526L04_MS1_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C052_200526L04_MS1_SCGE_FrD_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 C052_200526L04_MS1_SCGE_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C052_200526L04_MS1_SCGE_FrD_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 C052_200526L04_MS1_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C052_200526L04_MS1_SCGE_FrD_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 C052_200526L04_MS1_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C052_200526L04_MS1_SCGE_FrD_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 C053_200526L05_MS86_SCGE_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C053_200526L05_MS86_SCGE_FrA_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 C053_200526L05_MS86_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C053_200526L05_MS86_SCGE_FrA_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 C053_200526L05_MS86_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C053_200526L05_MS86_SCGE_FrA_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 C053_200526L05_MS86_SCGE_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C053_200526L05_MS86_SCGE_FrA_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 C053_200526L05_MS86_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C053_200526L05_MS86_SCGE_FrA_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 C053_200526L05_MS86_SCGE_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C053_200526L05_MS86_SCGE_FrA_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 C054_200526L06_MS86_SCGE_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C054_200526L06_MS86_SCGE_FrB_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 C054_200526L06_MS86_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C054_200526L06_MS86_SCGE_FrB_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 C054_200526L06_MS86_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C054_200526L06_MS86_SCGE_FrB_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 C054_200526L06_MS86_SCGE_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C054_200526L06_MS86_SCGE_FrB_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 C054_200526L06_MS86_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C054_200526L06_MS86_SCGE_FrB_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 C054_200526L06_MS86_SCGE_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C054_200526L06_MS86_SCGE_FrB_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 C055_200526L07_MS86_SCGE_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C055_200526L07_MS86_SCGE_FrC_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 C055_200526L07_MS86_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C055_200526L07_MS86_SCGE_FrC_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 C055_200526L07_MS86_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C055_200526L07_MS86_SCGE_FrC_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 C055_200526L07_MS86_SCGE_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C055_200526L07_MS86_SCGE_FrC_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 C055_200526L07_MS86_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C055_200526L07_MS86_SCGE_FrC_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 C055_200526L07_MS86_SCGE_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C055_200526L07_MS86_SCGE_FrC_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 C056_200526L08_MS86_SCGE_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C056_200526L08_MS86_SCGE_FrD_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 C056_200526L08_MS86_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C056_200526L08_MS86_SCGE_FrD_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 C056_200526L08_MS86_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C056_200526L08_MS86_SCGE_FrD_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 C056_200526L08_MS86_SCGE_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C056_200526L08_MS86_SCGE_FrD_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 C056_200526L08_MS86_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C056_200526L08_MS86_SCGE_FrD_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 C056_200526L08_MS86_SCGE_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C056_200526L08_MS86_SCGE_FrD_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 C057_200526L09_MS1_SCGE_FrA_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C057_200526L09_MS1_SCGE_FrA_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 C057_200526L09_MS1_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C057_200526L09_MS1_SCGE_FrA_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 C057_200526L09_MS1_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C057_200526L09_MS1_SCGE_FrA_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 C057_200526L09_MS1_SCGE_FrA_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C057_200526L09_MS1_SCGE_FrA_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 C057_200526L09_MS1_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C057_200526L09_MS1_SCGE_FrA_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 C057_200526L09_MS1_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C057_200526L09_MS1_SCGE_FrA_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C058_200526L10_MS1_SCGE_FrB_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C058_200526L10_MS1_SCGE_FrB_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 C058_200526L10_MS1_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C058_200526L10_MS1_SCGE_FrB_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 C058_200526L10_MS1_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C058_200526L10_MS1_SCGE_FrB_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 C058_200526L10_MS1_SCGE_FrB_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C058_200526L10_MS1_SCGE_FrB_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 C058_200526L10_MS1_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C058_200526L10_MS1_SCGE_FrB_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 C058_200526L10_MS1_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C058_200526L10_MS1_SCGE_FrB_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C059_200526L11_MS1_SCGE_FrC_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C059_200526L11_MS1_SCGE_FrC_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 C059_200526L11_MS1_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C059_200526L11_MS1_SCGE_FrC_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 C059_200526L11_MS1_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C059_200526L11_MS1_SCGE_FrC_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 C059_200526L11_MS1_SCGE_FrC_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C059_200526L11_MS1_SCGE_FrC_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 C059_200526L11_MS1_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C059_200526L11_MS1_SCGE_FrC_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 C059_200526L11_MS1_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C059_200526L11_MS1_SCGE_FrC_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C060_200526L12_MS1_SCGE_FrD_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C060_200526L12_MS1_SCGE_FrD_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 C060_200526L12_MS1_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C060_200526L12_MS1_SCGE_FrD_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 C060_200526L12_MS1_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C060_200526L12_MS1_SCGE_FrD_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 C060_200526L12_MS1_SCGE_FrD_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C060_200526L12_MS1_SCGE_FrD_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 C060_200526L12_MS1_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C060_200526L12_MS1_SCGE_FrD_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 C060_200526L12_MS1_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C060_200526L12_MS1_SCGE_FrD_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C061_200526L13_MS86_SCGE_FrA_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C061_200526L13_MS86_SCGE_FrA_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 C061_200526L13_MS86_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C061_200526L13_MS86_SCGE_FrA_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 C061_200526L13_MS86_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C061_200526L13_MS86_SCGE_FrA_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 C061_200526L13_MS86_SCGE_FrA_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C061_200526L13_MS86_SCGE_FrA_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 C061_200526L13_MS86_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C061_200526L13_MS86_SCGE_FrA_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 C061_200526L13_MS86_SCGE_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C061_200526L13_MS86_SCGE_FrA_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C062_200526L14_MS86_SCGE_FrB_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C062_200526L14_MS86_SCGE_FrB_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 C062_200526L14_MS86_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C062_200526L14_MS86_SCGE_FrB_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 C062_200526L14_MS86_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C062_200526L14_MS86_SCGE_FrB_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 C062_200526L14_MS86_SCGE_FrB_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C062_200526L14_MS86_SCGE_FrB_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 C062_200526L14_MS86_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C062_200526L14_MS86_SCGE_FrB_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 C062_200526L14_MS86_SCGE_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C062_200526L14_MS86_SCGE_FrB_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C063_200526L15_MS86_SCGE_FrC_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C063_200526L15_MS86_SCGE_FrC_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 C063_200526L15_MS86_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C063_200526L15_MS86_SCGE_FrC_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 C063_200526L15_MS86_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C063_200526L15_MS86_SCGE_FrC_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 C063_200526L15_MS86_SCGE_FrC_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C063_200526L15_MS86_SCGE_FrC_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 C063_200526L15_MS86_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C063_200526L15_MS86_SCGE_FrC_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 C063_200526L15_MS86_SCGE_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C063_200526L15_MS86_SCGE_FrC_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C064_200526L16_MS86_SCGE_FrD_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C064_200526L16_MS86_SCGE_FrD_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 C064_200526L16_MS86_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C064_200526L16_MS86_SCGE_FrD_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 C064_200526L16_MS86_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C064_200526L16_MS86_SCGE_FrD_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 C064_200526L16_MS86_SCGE_FrD_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C064_200526L16_MS86_SCGE_FrD_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 C064_200526L16_MS86_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C064_200526L16_MS86_SCGE_FrD_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 C064_200526L16_MS86_SCGE_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C064_200526L16_MS86_SCGE_FrD_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C065_200526L17_MS1_SCGE_FrA_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C065_200526L17_MS1_SCGE_FrA_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 C065_200526L17_MS1_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C065_200526L17_MS1_SCGE_FrA_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 C065_200526L17_MS1_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C065_200526L17_MS1_SCGE_FrA_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 C065_200526L17_MS1_SCGE_FrA_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C065_200526L17_MS1_SCGE_FrA_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 C065_200526L17_MS1_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C065_200526L17_MS1_SCGE_FrA_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 C065_200526L17_MS1_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C065_200526L17_MS1_SCGE_FrA_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 C066_200526L18_MS1_SCGE_FrB_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C066_200526L18_MS1_SCGE_FrB_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 C066_200526L18_MS1_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C066_200526L18_MS1_SCGE_FrB_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 C066_200526L18_MS1_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C066_200526L18_MS1_SCGE_FrB_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 C066_200526L18_MS1_SCGE_FrB_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C066_200526L18_MS1_SCGE_FrB_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 C066_200526L18_MS1_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C066_200526L18_MS1_SCGE_FrB_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 C066_200526L18_MS1_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C066_200526L18_MS1_SCGE_FrB_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 C067_200526L19_MS1_SCGE_FrC_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C067_200526L19_MS1_SCGE_FrC_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 C067_200526L19_MS1_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C067_200526L19_MS1_SCGE_FrC_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 C067_200526L19_MS1_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C067_200526L19_MS1_SCGE_FrC_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 C067_200526L19_MS1_SCGE_FrC_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C067_200526L19_MS1_SCGE_FrC_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 C067_200526L19_MS1_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C067_200526L19_MS1_SCGE_FrC_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 C067_200526L19_MS1_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C067_200526L19_MS1_SCGE_FrC_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 C068_200526L20_MS1_SCGE_FrD_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C068_200526L20_MS1_SCGE_FrD_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 C068_200526L20_MS1_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C068_200526L20_MS1_SCGE_FrD_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 C068_200526L20_MS1_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C068_200526L20_MS1_SCGE_FrD_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 C068_200526L20_MS1_SCGE_FrD_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C068_200526L20_MS1_SCGE_FrD_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 C068_200526L20_MS1_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C068_200526L20_MS1_SCGE_FrD_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 C068_200526L20_MS1_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C068_200526L20_MS1_SCGE_FrD_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 C069_200526L21_MS86_SCGE_FrA_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C069_200526L21_MS86_SCGE_FrA_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 C069_200526L21_MS86_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C069_200526L21_MS86_SCGE_FrA_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 C069_200526L21_MS86_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C069_200526L21_MS86_SCGE_FrA_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 C069_200526L21_MS86_SCGE_FrA_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C069_200526L21_MS86_SCGE_FrA_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 C069_200526L21_MS86_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C069_200526L21_MS86_SCGE_FrA_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 C069_200526L21_MS86_SCGE_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C069_200526L21_MS86_SCGE_FrA_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 C070_200526L22_MS86_SCGE_FrB_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C070_200526L22_MS86_SCGE_FrB_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 C070_200526L22_MS86_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C070_200526L22_MS86_SCGE_FrB_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 C070_200526L22_MS86_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C070_200526L22_MS86_SCGE_FrB_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 C070_200526L22_MS86_SCGE_FrB_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C070_200526L22_MS86_SCGE_FrB_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 C070_200526L22_MS86_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C070_200526L22_MS86_SCGE_FrB_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 C070_200526L22_MS86_SCGE_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C070_200526L22_MS86_SCGE_FrB_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 C071_200526L23_MS86_SCGE_FrC_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C071_200526L23_MS86_SCGE_FrC_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 C071_200526L23_MS86_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C071_200526L23_MS86_SCGE_FrC_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 C071_200526L23_MS86_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C071_200526L23_MS86_SCGE_FrC_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 C071_200526L23_MS86_SCGE_FrC_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C071_200526L23_MS86_SCGE_FrC_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 C071_200526L23_MS86_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C071_200526L23_MS86_SCGE_FrC_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 C071_200526L23_MS86_SCGE_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C071_200526L23_MS86_SCGE_FrC_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 C072_200526L24_MS86_SCGE_FrD_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C072_200526L24_MS86_SCGE_FrD_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 C072_200526L24_MS86_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C072_200526L24_MS86_SCGE_FrD_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 C072_200526L24_MS86_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C072_200526L24_MS86_SCGE_FrD_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 C072_200526L24_MS86_SCGE_FrD_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C072_200526L24_MS86_SCGE_FrD_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 C072_200526L24_MS86_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C072_200526L24_MS86_SCGE_FrD_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 C072_200526L24_MS86_SCGE_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C072_200526L24_MS86_SCGE_FrD_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 C073_190923L59_exp190909_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C073_190923L59_exp190909_MS88_FrA_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 C073_190923L59_exp190909_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C073_190923L59_exp190909_MS88_FrA_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 C073_190923L59_exp190909_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C073_190923L59_exp190909_MS88_FrA_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 C073_190923L59_exp190909_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C073_190923L59_exp190909_MS88_FrA_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 C073_190923L59_exp190909_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C073_190923L59_exp190909_MS88_FrA_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 C073_190923L59_exp190909_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C073_190923L59_exp190909_MS88_FrA_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 C074_190923L60_exp190909_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C074_190923L60_exp190909_MS88_FrB_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 C074_190923L60_exp190909_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C074_190923L60_exp190909_MS88_FrB_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 C074_190923L60_exp190909_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C074_190923L60_exp190909_MS88_FrB_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 C074_190923L60_exp190909_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C074_190923L60_exp190909_MS88_FrB_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 C074_190923L60_exp190909_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C074_190923L60_exp190909_MS88_FrB_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 C074_190923L60_exp190909_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C074_190923L60_exp190909_MS88_FrB_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 C075_190923L61_exp190909_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C075_190923L61_exp190909_MS88_FrC_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 C075_190923L61_exp190909_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C075_190923L61_exp190909_MS88_FrC_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 C075_190923L61_exp190909_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C075_190923L61_exp190909_MS88_FrC_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 C075_190923L61_exp190909_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C075_190923L61_exp190909_MS88_FrC_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 C075_190923L61_exp190909_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C075_190923L61_exp190909_MS88_FrC_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 C075_190923L61_exp190909_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C075_190923L61_exp190909_MS88_FrC_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 C076_190923L62_exp190909_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C076_190923L62_exp190909_MS88_FrD_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 C076_190923L62_exp190909_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C076_190923L62_exp190909_MS88_FrD_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 C076_190923L62_exp190909_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C076_190923L62_exp190909_MS88_FrD_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 C076_190923L62_exp190909_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C076_190923L62_exp190909_MS88_FrD_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 C076_190923L62_exp190909_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C076_190923L62_exp190909_MS88_FrD_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 C076_190923L62_exp190909_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C076_190923L62_exp190909_MS88_FrD_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 C077_190923L63_exp190909_MS88_FrA_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C077_190923L63_exp190909_MS88_FrA_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 C077_190923L63_exp190909_MS88_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C077_190923L63_exp190909_MS88_FrA_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 C077_190923L63_exp190909_MS88_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C077_190923L63_exp190909_MS88_FrA_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 C077_190923L63_exp190909_MS88_FrA_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C077_190923L63_exp190909_MS88_FrA_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 C077_190923L63_exp190909_MS88_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C077_190923L63_exp190909_MS88_FrA_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 C077_190923L63_exp190909_MS88_FrA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C077_190923L63_exp190909_MS88_FrA_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 C078_190923L64_exp190909_MS88_FrB_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C078_190923L64_exp190909_MS88_FrB_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 C078_190923L64_exp190909_MS88_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C078_190923L64_exp190909_MS88_FrB_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 C078_190923L64_exp190909_MS88_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C078_190923L64_exp190909_MS88_FrB_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 C078_190923L64_exp190909_MS88_FrB_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C078_190923L64_exp190909_MS88_FrB_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 C078_190923L64_exp190909_MS88_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C078_190923L64_exp190909_MS88_FrB_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 C078_190923L64_exp190909_MS88_FrB_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C078_190923L64_exp190909_MS88_FrB_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 C079_190923L65_exp190909_MS88_FrC_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C079_190923L65_exp190909_MS88_FrC_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 C079_190923L65_exp190909_MS88_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C079_190923L65_exp190909_MS88_FrC_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 C079_190923L65_exp190909_MS88_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C079_190923L65_exp190909_MS88_FrC_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 C079_190923L65_exp190909_MS88_FrC_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C079_190923L65_exp190909_MS88_FrC_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 C079_190923L65_exp190909_MS88_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C079_190923L65_exp190909_MS88_FrC_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 C079_190923L65_exp190909_MS88_FrC_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C079_190923L65_exp190909_MS88_FrC_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 C080_190923L66_exp190909_MS88_FrD_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C080_190923L66_exp190909_MS88_FrD_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 C080_190923L66_exp190909_MS88_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C080_190923L66_exp190909_MS88_FrD_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 C080_190923L66_exp190909_MS88_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C080_190923L66_exp190909_MS88_FrD_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 C080_190923L66_exp190909_MS88_FrD_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C080_190923L66_exp190909_MS88_FrD_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 C080_190923L66_exp190909_MS88_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C080_190923L66_exp190909_MS88_FrD_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 C080_190923L66_exp190909_MS88_FrD_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C080_190923L66_exp190909_MS88_FrD_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 C081_190923L83_exp190909_MS88_FrD_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C081_190923L83_exp190909_MS88_FrD_AB01_R.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 C081_190923L83_exp190909_MS88_FrD_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C081_190923L83_exp190909_MS88_FrD_AB01_R.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 C081_190923L83_exp190909_MS88_FrD_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C081_190923L83_exp190909_MS88_FrD_AB01_R.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 C081_190923L83_exp190909_MS88_FrD_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C081_190923L83_exp190909_MS88_FrD_AB01_R.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 C081_190923L83_exp190909_MS88_FrD_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C081_190923L83_exp190909_MS88_FrD_AB01_R.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 C081_190923L83_exp190909_MS88_FrD_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C081_190923L83_exp190909_MS88_FrD_AB01_R.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 C082_190923L67_exp190909_MS88_FrA_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C082_190923L67_exp190909_MS88_FrA_AB04.1x36mers.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 C082_190923L67_exp190909_MS88_FrA_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C082_190923L67_exp190909_MS88_FrA_AB04.2x36mers.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 C082_190923L67_exp190909_MS88_FrA_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C082_190923L67_exp190909_MS88_FrA_AB04.2x36mers.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 C082_190923L67_exp190909_MS88_FrA_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C082_190923L67_exp190909_MS88_FrA_AB04.1x36mers.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 C082_190923L67_exp190909_MS88_FrA_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C082_190923L67_exp190909_MS88_FrA_AB04.2x36mers.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 C082_190923L67_exp190909_MS88_FrA_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C082_190923L67_exp190909_MS88_FrA_AB04.2x36mers.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 C083_190923L68_exp190909_MS88_FrB_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C083_190923L68_exp190909_MS88_FrB_AB04.1x36mers.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 C083_190923L68_exp190909_MS88_FrB_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C083_190923L68_exp190909_MS88_FrB_AB04.2x36mers.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 C083_190923L68_exp190909_MS88_FrB_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C083_190923L68_exp190909_MS88_FrB_AB04.2x36mers.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 C083_190923L68_exp190909_MS88_FrB_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C083_190923L68_exp190909_MS88_FrB_AB04.1x36mers.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 C083_190923L68_exp190909_MS88_FrB_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C083_190923L68_exp190909_MS88_FrB_AB04.2x36mers.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 C083_190923L68_exp190909_MS88_FrB_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C083_190923L68_exp190909_MS88_FrB_AB04.2x36mers.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 C084_190923L69_exp190909_MS88_FrC_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C084_190923L69_exp190909_MS88_FrC_AB04.1x36mers.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 C084_190923L69_exp190909_MS88_FrC_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C084_190923L69_exp190909_MS88_FrC_AB04.2x36mers.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 C084_190923L69_exp190909_MS88_FrC_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C084_190923L69_exp190909_MS88_FrC_AB04.2x36mers.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 C084_190923L69_exp190909_MS88_FrC_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C084_190923L69_exp190909_MS88_FrC_AB04.1x36mers.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 C084_190923L69_exp190909_MS88_FrC_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C084_190923L69_exp190909_MS88_FrC_AB04.2x36mers.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 C084_190923L69_exp190909_MS88_FrC_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C084_190923L69_exp190909_MS88_FrC_AB04.2x36mers.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 C085_190923L70_exp190909_MS88_FrD_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C085_190923L70_exp190909_MS88_FrD_AB04.1x36mers.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 C085_190923L70_exp190909_MS88_FrD_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C085_190923L70_exp190909_MS88_FrD_AB04.2x36mers.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 C085_190923L70_exp190909_MS88_FrD_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C085_190923L70_exp190909_MS88_FrD_AB04.2x36mers.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 C085_190923L70_exp190909_MS88_FrD_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C085_190923L70_exp190909_MS88_FrD_AB04.1x36mers.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 C085_190923L70_exp190909_MS88_FrD_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C085_190923L70_exp190909_MS88_FrD_AB04.2x36mers.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 C085_190923L70_exp190909_MS88_FrD_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C085_190923L70_exp190909_MS88_FrD_AB04.2x36mers.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 C086_190923L71_exp190909_MS88_FrA_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C086_190923L71_exp190909_MS88_FrA_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 C086_190923L71_exp190909_MS88_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C086_190923L71_exp190909_MS88_FrA_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 C086_190923L71_exp190909_MS88_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C086_190923L71_exp190909_MS88_FrA_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 C086_190923L71_exp190909_MS88_FrA_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C086_190923L71_exp190909_MS88_FrA_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 C086_190923L71_exp190909_MS88_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C086_190923L71_exp190909_MS88_FrA_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 C086_190923L71_exp190909_MS88_FrA_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C086_190923L71_exp190909_MS88_FrA_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C087_190923L72_exp190909_MS88_FrB_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C087_190923L72_exp190909_MS88_FrB_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 C087_190923L72_exp190909_MS88_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C087_190923L72_exp190909_MS88_FrB_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 C087_190923L72_exp190909_MS88_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C087_190923L72_exp190909_MS88_FrB_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 C087_190923L72_exp190909_MS88_FrB_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C087_190923L72_exp190909_MS88_FrB_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 C087_190923L72_exp190909_MS88_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C087_190923L72_exp190909_MS88_FrB_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 C087_190923L72_exp190909_MS88_FrB_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C087_190923L72_exp190909_MS88_FrB_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C088_190923L73_exp190909_MS88_FrC_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C088_190923L73_exp190909_MS88_FrC_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 C088_190923L73_exp190909_MS88_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C088_190923L73_exp190909_MS88_FrC_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 C088_190923L73_exp190909_MS88_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C088_190923L73_exp190909_MS88_FrC_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 C088_190923L73_exp190909_MS88_FrC_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C088_190923L73_exp190909_MS88_FrC_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 C088_190923L73_exp190909_MS88_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C088_190923L73_exp190909_MS88_FrC_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 C088_190923L73_exp190909_MS88_FrC_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C088_190923L73_exp190909_MS88_FrC_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C089_190923L74_exp190909_MS88_FrD_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C089_190923L74_exp190909_MS88_FrD_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 C089_190923L74_exp190909_MS88_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C089_190923L74_exp190909_MS88_FrD_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 C089_190923L74_exp190909_MS88_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C089_190923L74_exp190909_MS88_FrD_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 C089_190923L74_exp190909_MS88_FrD_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C089_190923L74_exp190909_MS88_FrD_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 C089_190923L74_exp190909_MS88_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C089_190923L74_exp190909_MS88_FrD_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 C089_190923L74_exp190909_MS88_FrD_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C089_190923L74_exp190909_MS88_FrD_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py C090_190923L75_exp190909_MS88_FrA_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C090_190923L75_exp190909_MS88_FrA_AB21.1x36mers.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 C090_190923L75_exp190909_MS88_FrA_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C090_190923L75_exp190909_MS88_FrA_AB21.2x36mers.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 C090_190923L75_exp190909_MS88_FrA_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C090_190923L75_exp190909_MS88_FrA_AB21.2x36mers.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 C090_190923L75_exp190909_MS88_FrA_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C090_190923L75_exp190909_MS88_FrA_AB21.1x36mers.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 C090_190923L75_exp190909_MS88_FrA_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C090_190923L75_exp190909_MS88_FrA_AB21.2x36mers.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 C090_190923L75_exp190909_MS88_FrA_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C090_190923L75_exp190909_MS88_FrA_AB21.2x36mers.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 C091_190923L76_exp190909_MS88_FrB_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C091_190923L76_exp190909_MS88_FrB_AB21.1x36mers.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 C091_190923L76_exp190909_MS88_FrB_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C091_190923L76_exp190909_MS88_FrB_AB21.2x36mers.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 C091_190923L76_exp190909_MS88_FrB_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C091_190923L76_exp190909_MS88_FrB_AB21.2x36mers.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 C091_190923L76_exp190909_MS88_FrB_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C091_190923L76_exp190909_MS88_FrB_AB21.1x36mers.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 C091_190923L76_exp190909_MS88_FrB_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C091_190923L76_exp190909_MS88_FrB_AB21.2x36mers.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 C091_190923L76_exp190909_MS88_FrB_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C091_190923L76_exp190909_MS88_FrB_AB21.2x36mers.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 C092_190923L77_exp190909_MS88_FrC_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C092_190923L77_exp190909_MS88_FrC_AB21.1x36mers.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 C092_190923L77_exp190909_MS88_FrC_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C092_190923L77_exp190909_MS88_FrC_AB21.2x36mers.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 C092_190923L77_exp190909_MS88_FrC_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C092_190923L77_exp190909_MS88_FrC_AB21.2x36mers.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 C092_190923L77_exp190909_MS88_FrC_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C092_190923L77_exp190909_MS88_FrC_AB21.1x36mers.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 C092_190923L77_exp190909_MS88_FrC_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C092_190923L77_exp190909_MS88_FrC_AB21.2x36mers.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 C092_190923L77_exp190909_MS88_FrC_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C092_190923L77_exp190909_MS88_FrC_AB21.2x36mers.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 C093_190923L78_exp190909_MS88_FrD_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C093_190923L78_exp190909_MS88_FrD_AB21.1x36mers.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 C093_190923L78_exp190909_MS88_FrD_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C093_190923L78_exp190909_MS88_FrD_AB21.2x36mers.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 C093_190923L78_exp190909_MS88_FrD_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C093_190923L78_exp190909_MS88_FrD_AB21.2x36mers.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 C093_190923L78_exp190909_MS88_FrD_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-C093_190923L78_exp190909_MS88_FrD_AB21.1x36mers.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 C093_190923L78_exp190909_MS88_FrD_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C093_190923L78_exp190909_MS88_FrD_AB21.2x36mers.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 C093_190923L78_exp190909_MS88_FrD_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-C093_190923L78_exp190909_MS88_FrD_AB21.2x36mers.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 D001_181105L01_exp180711_MS1_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D001_181105L01_exp180711_MS1_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 D001_181105L01_exp180711_MS1_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D001_181105L01_exp180711_MS1_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 D001_181105L01_exp180711_MS1_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D001_181105L01_exp180711_MS1_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 D001_181105L01_exp180711_MS1_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D001_181105L01_exp180711_MS1_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 D001_181105L01_exp180711_MS1_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D001_181105L01_exp180711_MS1_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 D001_181105L01_exp180711_MS1_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D001_181105L01_exp180711_MS1_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 D002_181105L02_exp180711_MS80_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D002_181105L02_exp180711_MS80_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 D002_181105L02_exp180711_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D002_181105L02_exp180711_MS80_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 D002_181105L02_exp180711_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D002_181105L02_exp180711_MS80_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 D002_181105L02_exp180711_MS80_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D002_181105L02_exp180711_MS80_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 D002_181105L02_exp180711_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D002_181105L02_exp180711_MS80_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 D002_181105L02_exp180711_MS80_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D002_181105L02_exp180711_MS80_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 D003_181105L03_exp180711_MS81_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D003_181105L03_exp180711_MS81_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 D003_181105L03_exp180711_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D003_181105L03_exp180711_MS81_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 D003_181105L03_exp180711_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D003_181105L03_exp180711_MS81_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 D003_181105L03_exp180711_MS81_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D003_181105L03_exp180711_MS81_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 D003_181105L03_exp180711_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D003_181105L03_exp180711_MS81_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 D003_181105L03_exp180711_MS81_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D003_181105L03_exp180711_MS81_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 D004_181105L04_exp180712_MS63_SCGE-0nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D004_181105L04_exp180712_MS63_SCGE-0nM-BE_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 D004_181105L04_exp180712_MS63_SCGE-0nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D004_181105L04_exp180712_MS63_SCGE-0nM-BE_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 D004_181105L04_exp180712_MS63_SCGE-0nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D004_181105L04_exp180712_MS63_SCGE-0nM-BE_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 D004_181105L04_exp180712_MS63_SCGE-0nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D004_181105L04_exp180712_MS63_SCGE-0nM-BE_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 D004_181105L04_exp180712_MS63_SCGE-0nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D004_181105L04_exp180712_MS63_SCGE-0nM-BE_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 D004_181105L04_exp180712_MS63_SCGE-0nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D004_181105L04_exp180712_MS63_SCGE-0nM-BE_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 D005_181105L05_exp180712_MS63_SCGE-10nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D005_181105L05_exp180712_MS63_SCGE-10nM-BE_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 D005_181105L05_exp180712_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D005_181105L05_exp180712_MS63_SCGE-10nM-BE_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 D005_181105L05_exp180712_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D005_181105L05_exp180712_MS63_SCGE-10nM-BE_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 D005_181105L05_exp180712_MS63_SCGE-10nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D005_181105L05_exp180712_MS63_SCGE-10nM-BE_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 D005_181105L05_exp180712_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D005_181105L05_exp180712_MS63_SCGE-10nM-BE_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 D005_181105L05_exp180712_MS63_SCGE-10nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D005_181105L05_exp180712_MS63_SCGE-10nM-BE_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 D006_181105L06_exp180712_MS63_SCGE-30nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D006_181105L06_exp180712_MS63_SCGE-30nM-BE_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 D006_181105L06_exp180712_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D006_181105L06_exp180712_MS63_SCGE-30nM-BE_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 D006_181105L06_exp180712_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D006_181105L06_exp180712_MS63_SCGE-30nM-BE_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 D006_181105L06_exp180712_MS63_SCGE-30nM-BE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D006_181105L06_exp180712_MS63_SCGE-30nM-BE_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 D006_181105L06_exp180712_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D006_181105L06_exp180712_MS63_SCGE-30nM-BE_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 D006_181105L06_exp180712_MS63_SCGE-30nM-BE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D006_181105L06_exp180712_MS63_SCGE-30nM-BE_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 D007_181105L07_exp180711_MS1_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D007_181105L07_exp180711_MS1_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 D007_181105L07_exp180711_MS1_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D007_181105L07_exp180711_MS1_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 D007_181105L07_exp180711_MS1_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D007_181105L07_exp180711_MS1_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 D007_181105L07_exp180711_MS1_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D007_181105L07_exp180711_MS1_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 D007_181105L07_exp180711_MS1_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D007_181105L07_exp180711_MS1_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 D007_181105L07_exp180711_MS1_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D007_181105L07_exp180711_MS1_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py D008_181105L08_exp180711_MS80_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D008_181105L08_exp180711_MS80_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 D008_181105L08_exp180711_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D008_181105L08_exp180711_MS80_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 D008_181105L08_exp180711_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D008_181105L08_exp180711_MS80_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 D008_181105L08_exp180711_MS80_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D008_181105L08_exp180711_MS80_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 D008_181105L08_exp180711_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D008_181105L08_exp180711_MS80_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 D008_181105L08_exp180711_MS80_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D008_181105L08_exp180711_MS80_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py D009_181105L09_exp180711_MS81_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D009_181105L09_exp180711_MS81_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 D009_181105L09_exp180711_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D009_181105L09_exp180711_MS81_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 D009_181105L09_exp180711_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D009_181105L09_exp180711_MS81_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 D009_181105L09_exp180711_MS81_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D009_181105L09_exp180711_MS81_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 D009_181105L09_exp180711_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D009_181105L09_exp180711_MS81_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 D009_181105L09_exp180711_MS81_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D009_181105L09_exp180711_MS81_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py D010_181105L10_exp180712_MS63_SCGE-0nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D010_181105L10_exp180712_MS63_SCGE-0nM-BE_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 D010_181105L10_exp180712_MS63_SCGE-0nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D010_181105L10_exp180712_MS63_SCGE-0nM-BE_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 D010_181105L10_exp180712_MS63_SCGE-0nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D010_181105L10_exp180712_MS63_SCGE-0nM-BE_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 D010_181105L10_exp180712_MS63_SCGE-0nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D010_181105L10_exp180712_MS63_SCGE-0nM-BE_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 D010_181105L10_exp180712_MS63_SCGE-0nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D010_181105L10_exp180712_MS63_SCGE-0nM-BE_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 D010_181105L10_exp180712_MS63_SCGE-0nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D010_181105L10_exp180712_MS63_SCGE-0nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py D011_181105L11_exp180712_MS63_SCGE-10nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D011_181105L11_exp180712_MS63_SCGE-10nM-BE_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 D011_181105L11_exp180712_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D011_181105L11_exp180712_MS63_SCGE-10nM-BE_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 D011_181105L11_exp180712_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D011_181105L11_exp180712_MS63_SCGE-10nM-BE_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 D011_181105L11_exp180712_MS63_SCGE-10nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D011_181105L11_exp180712_MS63_SCGE-10nM-BE_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 D011_181105L11_exp180712_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D011_181105L11_exp180712_MS63_SCGE-10nM-BE_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 D011_181105L11_exp180712_MS63_SCGE-10nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D011_181105L11_exp180712_MS63_SCGE-10nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py D012_181105L12_exp180712_MS63_SCGE-30nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D012_181105L12_exp180712_MS63_SCGE-30nM-BE_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 D012_181105L12_exp180712_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D012_181105L12_exp180712_MS63_SCGE-30nM-BE_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 D012_181105L12_exp180712_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D012_181105L12_exp180712_MS63_SCGE-30nM-BE_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 D012_181105L12_exp180712_MS63_SCGE-30nM-BE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D012_181105L12_exp180712_MS63_SCGE-30nM-BE_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 D012_181105L12_exp180712_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D012_181105L12_exp180712_MS63_SCGE-30nM-BE_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 D012_181105L12_exp180712_MS63_SCGE-30nM-BE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D012_181105L12_exp180712_MS63_SCGE-30nM-BE_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py D013_181105L13_exp180711_MS1_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D013_181105L13_exp180711_MS1_SCGE_AB21.1x36mers.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 D013_181105L13_exp180711_MS1_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D013_181105L13_exp180711_MS1_SCGE_AB21.2x36mers.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 D013_181105L13_exp180711_MS1_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D013_181105L13_exp180711_MS1_SCGE_AB21.2x36mers.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 D013_181105L13_exp180711_MS1_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D013_181105L13_exp180711_MS1_SCGE_AB21.1x36mers.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 D013_181105L13_exp180711_MS1_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D013_181105L13_exp180711_MS1_SCGE_AB21.2x36mers.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 D013_181105L13_exp180711_MS1_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D013_181105L13_exp180711_MS1_SCGE_AB21.2x36mers.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 D014_181105L14_exp180711_MS80_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D014_181105L14_exp180711_MS80_SCGE_AB21.1x36mers.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 D014_181105L14_exp180711_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D014_181105L14_exp180711_MS80_SCGE_AB21.2x36mers.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 D014_181105L14_exp180711_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D014_181105L14_exp180711_MS80_SCGE_AB21.2x36mers.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 D014_181105L14_exp180711_MS80_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D014_181105L14_exp180711_MS80_SCGE_AB21.1x36mers.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 D014_181105L14_exp180711_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D014_181105L14_exp180711_MS80_SCGE_AB21.2x36mers.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 D014_181105L14_exp180711_MS80_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D014_181105L14_exp180711_MS80_SCGE_AB21.2x36mers.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 D015_181105L15_exp180711_MS81_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D015_181105L15_exp180711_MS81_SCGE_AB21.1x36mers.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 D015_181105L15_exp180711_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D015_181105L15_exp180711_MS81_SCGE_AB21.2x36mers.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 D015_181105L15_exp180711_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D015_181105L15_exp180711_MS81_SCGE_AB21.2x36mers.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 D015_181105L15_exp180711_MS81_SCGE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D015_181105L15_exp180711_MS81_SCGE_AB21.1x36mers.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 D015_181105L15_exp180711_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D015_181105L15_exp180711_MS81_SCGE_AB21.2x36mers.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 D015_181105L15_exp180711_MS81_SCGE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D015_181105L15_exp180711_MS81_SCGE_AB21.2x36mers.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 D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.1x36mers.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 D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.2x36mers.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 D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.2x36mers.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 D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.1x36mers.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 D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.2x36mers.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 D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D016_181105L16_exp180712_MS63_SCGE-0nM-BE_AB21.2x36mers.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 D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.1x36mers.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 D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.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 D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.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 D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.1x36mers.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 D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.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 D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D017_181105L17_exp180712_MS63_SCGE-10nM-BE_AB21.2x36mers.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 D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.1x36mers.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 D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.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 D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.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 D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.1x36mers.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 D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.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 D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D018_181105L18_exp180712_MS63_SCGE-30nM-BE_AB21.2x36mers.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 D019_181105L19_exp180711_MS1_SCGE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D019_181105L19_exp180711_MS1_SCGE_AB39.1x36mers.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 D019_181105L19_exp180711_MS1_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D019_181105L19_exp180711_MS1_SCGE_AB39.2x36mers.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 D019_181105L19_exp180711_MS1_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D019_181105L19_exp180711_MS1_SCGE_AB39.2x36mers.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 D019_181105L19_exp180711_MS1_SCGE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D019_181105L19_exp180711_MS1_SCGE_AB39.1x36mers.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 D019_181105L19_exp180711_MS1_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D019_181105L19_exp180711_MS1_SCGE_AB39.2x36mers.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 D019_181105L19_exp180711_MS1_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D019_181105L19_exp180711_MS1_SCGE_AB39.2x36mers.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 D020_181105L20_exp180711_MS80_SCGE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D020_181105L20_exp180711_MS80_SCGE_AB39.1x36mers.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 D020_181105L20_exp180711_MS80_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D020_181105L20_exp180711_MS80_SCGE_AB39.2x36mers.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 D020_181105L20_exp180711_MS80_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D020_181105L20_exp180711_MS80_SCGE_AB39.2x36mers.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 D020_181105L20_exp180711_MS80_SCGE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D020_181105L20_exp180711_MS80_SCGE_AB39.1x36mers.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 D020_181105L20_exp180711_MS80_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D020_181105L20_exp180711_MS80_SCGE_AB39.2x36mers.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 D020_181105L20_exp180711_MS80_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D020_181105L20_exp180711_MS80_SCGE_AB39.2x36mers.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 D021_181105L21_exp180711_MS81_SCGE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D021_181105L21_exp180711_MS81_SCGE_AB39.1x36mers.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 D021_181105L21_exp180711_MS81_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D021_181105L21_exp180711_MS81_SCGE_AB39.2x36mers.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 D021_181105L21_exp180711_MS81_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D021_181105L21_exp180711_MS81_SCGE_AB39.2x36mers.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 D021_181105L21_exp180711_MS81_SCGE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D021_181105L21_exp180711_MS81_SCGE_AB39.1x36mers.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 D021_181105L21_exp180711_MS81_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D021_181105L21_exp180711_MS81_SCGE_AB39.2x36mers.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 D021_181105L21_exp180711_MS81_SCGE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D021_181105L21_exp180711_MS81_SCGE_AB39.2x36mers.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 D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.1x36mers.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 D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.2x36mers.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 D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.2x36mers.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 D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.1x36mers.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 D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.2x36mers.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 D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D022_181105L22_exp180712_MS63_SCGE-0nM-BE_AB39.2x36mers.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 D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.1x36mers.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 D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.2x36mers.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 D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.2x36mers.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 D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.1x36mers.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 D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.2x36mers.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 D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D023_181105L23_exp180712_MS63_SCGE-10nM-BE_AB39.2x36mers.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 D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.1x36mers.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 D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.2x36mers.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 D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.2x36mers.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 D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.1x36mers.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 D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.2x36mers.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 D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D024_181105L24_exp180712_MS63_SCGE-30nM-BE_AB39.2x36mers.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 D025_181105L25_exp180711_MS1_SCGE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D025_181105L25_exp180711_MS1_SCGE_AB41.1x36mers.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 D025_181105L25_exp180711_MS1_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D025_181105L25_exp180711_MS1_SCGE_AB41.2x36mers.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 D025_181105L25_exp180711_MS1_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D025_181105L25_exp180711_MS1_SCGE_AB41.2x36mers.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 D025_181105L25_exp180711_MS1_SCGE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D025_181105L25_exp180711_MS1_SCGE_AB41.1x36mers.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 D025_181105L25_exp180711_MS1_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D025_181105L25_exp180711_MS1_SCGE_AB41.2x36mers.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 D025_181105L25_exp180711_MS1_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D025_181105L25_exp180711_MS1_SCGE_AB41.2x36mers.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 D026_181105L26_exp180711_MS80_SCGE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D026_181105L26_exp180711_MS80_SCGE_AB41.1x36mers.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 D026_181105L26_exp180711_MS80_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D026_181105L26_exp180711_MS80_SCGE_AB41.2x36mers.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 D026_181105L26_exp180711_MS80_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D026_181105L26_exp180711_MS80_SCGE_AB41.2x36mers.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 D026_181105L26_exp180711_MS80_SCGE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D026_181105L26_exp180711_MS80_SCGE_AB41.1x36mers.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 D026_181105L26_exp180711_MS80_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D026_181105L26_exp180711_MS80_SCGE_AB41.2x36mers.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 D026_181105L26_exp180711_MS80_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D026_181105L26_exp180711_MS80_SCGE_AB41.2x36mers.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 D027_181105L27_exp180711_MS81_SCGE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D027_181105L27_exp180711_MS81_SCGE_AB42.1x36mers.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 D027_181105L27_exp180711_MS81_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D027_181105L27_exp180711_MS81_SCGE_AB42.2x36mers.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 D027_181105L27_exp180711_MS81_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D027_181105L27_exp180711_MS81_SCGE_AB42.2x36mers.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 D027_181105L27_exp180711_MS81_SCGE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D027_181105L27_exp180711_MS81_SCGE_AB42.1x36mers.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 D027_181105L27_exp180711_MS81_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D027_181105L27_exp180711_MS81_SCGE_AB42.2x36mers.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 D027_181105L27_exp180711_MS81_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D027_181105L27_exp180711_MS81_SCGE_AB42.2x36mers.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 D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.1x36mers.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 D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.2x36mers.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 D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.2x36mers.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 D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.1x36mers.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 D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.2x36mers.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 D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D028_181105L28_exp180712_MS63_SCGE-0nM-BE_AB41.2x36mers.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 D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.1x36mers.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 D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.2x36mers.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 D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.2x36mers.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 D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.1x36mers.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 D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.2x36mers.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 D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D029_181105L29_exp180712_MS63_SCGE-10nM-BE_AB41.2x36mers.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 D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.1x36mers.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 D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.2x36mers.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 D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.2x36mers.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 D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.1x36mers.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 D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.2x36mers.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 D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D030_181105L30_exp180712_MS63_SCGE-30nM-BE_AB41.2x36mers.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 D031_181105L31_exp180711_MS1_SCGE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D031_181105L31_exp180711_MS1_SCGE_AB42.1x36mers.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 D031_181105L31_exp180711_MS1_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D031_181105L31_exp180711_MS1_SCGE_AB42.2x36mers.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 D031_181105L31_exp180711_MS1_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D031_181105L31_exp180711_MS1_SCGE_AB42.2x36mers.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 D031_181105L31_exp180711_MS1_SCGE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D031_181105L31_exp180711_MS1_SCGE_AB42.1x36mers.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 D031_181105L31_exp180711_MS1_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D031_181105L31_exp180711_MS1_SCGE_AB42.2x36mers.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 D031_181105L31_exp180711_MS1_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D031_181105L31_exp180711_MS1_SCGE_AB42.2x36mers.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 D032_181105L32_exp180711_MS80_SCGE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D032_181105L32_exp180711_MS80_SCGE_AB42.1x36mers.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 D032_181105L32_exp180711_MS80_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D032_181105L32_exp180711_MS80_SCGE_AB42.2x36mers.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 D032_181105L32_exp180711_MS80_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D032_181105L32_exp180711_MS80_SCGE_AB42.2x36mers.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 D032_181105L32_exp180711_MS80_SCGE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D032_181105L32_exp180711_MS80_SCGE_AB42.1x36mers.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 D032_181105L32_exp180711_MS80_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D032_181105L32_exp180711_MS80_SCGE_AB42.2x36mers.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 D032_181105L32_exp180711_MS80_SCGE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D032_181105L32_exp180711_MS80_SCGE_AB42.2x36mers.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 D033_181105L33_exp180711_MS81_SCGE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D033_181105L33_exp180711_MS81_SCGE_AB41.1x36mers.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 D033_181105L33_exp180711_MS81_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D033_181105L33_exp180711_MS81_SCGE_AB41.2x36mers.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 D033_181105L33_exp180711_MS81_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D033_181105L33_exp180711_MS81_SCGE_AB41.2x36mers.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 D033_181105L33_exp180711_MS81_SCGE_AB41.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D033_181105L33_exp180711_MS81_SCGE_AB41.1x36mers.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 D033_181105L33_exp180711_MS81_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D033_181105L33_exp180711_MS81_SCGE_AB41.2x36mers.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 D033_181105L33_exp180711_MS81_SCGE_AB41.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D033_181105L33_exp180711_MS81_SCGE_AB41.2x36mers.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 D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.1x36mers.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 D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.2x36mers.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 D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.2x36mers.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 D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.1x36mers.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 D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.2x36mers.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 D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D034_181105L34_exp180712_MS63_SCGE-0nM-BE_AB42.2x36mers.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 D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.1x36mers.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 D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.2x36mers.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 D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.2x36mers.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 D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.1x36mers.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 D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.2x36mers.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 D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D035_181105L35_exp180712_MS63_SCGE-10nM-BE_AB42.2x36mers.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 D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.1x36mers.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 D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.2x36mers.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 D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.2x36mers.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 D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.1x36mers.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 D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.2x36mers.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 D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D036_181105L36_exp180712_MS63_SCGE-30nM-BE_AB42.2x36mers.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 D037_181105L37_exp180711_MS1_SCGE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D037_181105L37_exp180711_MS1_SCGE_AB43.1x36mers.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 D037_181105L37_exp180711_MS1_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D037_181105L37_exp180711_MS1_SCGE_AB43.2x36mers.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 D037_181105L37_exp180711_MS1_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D037_181105L37_exp180711_MS1_SCGE_AB43.2x36mers.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 D037_181105L37_exp180711_MS1_SCGE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D037_181105L37_exp180711_MS1_SCGE_AB43.1x36mers.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 D037_181105L37_exp180711_MS1_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D037_181105L37_exp180711_MS1_SCGE_AB43.2x36mers.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 D037_181105L37_exp180711_MS1_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D037_181105L37_exp180711_MS1_SCGE_AB43.2x36mers.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 D038_181105L38_exp180711_MS80_SCGE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D038_181105L38_exp180711_MS80_SCGE_AB43.1x36mers.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 D038_181105L38_exp180711_MS80_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D038_181105L38_exp180711_MS80_SCGE_AB43.2x36mers.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 D038_181105L38_exp180711_MS80_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D038_181105L38_exp180711_MS80_SCGE_AB43.2x36mers.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 D038_181105L38_exp180711_MS80_SCGE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D038_181105L38_exp180711_MS80_SCGE_AB43.1x36mers.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 D038_181105L38_exp180711_MS80_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D038_181105L38_exp180711_MS80_SCGE_AB43.2x36mers.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 D038_181105L38_exp180711_MS80_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D038_181105L38_exp180711_MS80_SCGE_AB43.2x36mers.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 D039_181105L39_exp180711_MS81_SCGE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D039_181105L39_exp180711_MS81_SCGE_AB43.1x36mers.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 D039_181105L39_exp180711_MS81_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D039_181105L39_exp180711_MS81_SCGE_AB43.2x36mers.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 D039_181105L39_exp180711_MS81_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D039_181105L39_exp180711_MS81_SCGE_AB43.2x36mers.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 D039_181105L39_exp180711_MS81_SCGE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D039_181105L39_exp180711_MS81_SCGE_AB43.1x36mers.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 D039_181105L39_exp180711_MS81_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D039_181105L39_exp180711_MS81_SCGE_AB43.2x36mers.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 D039_181105L39_exp180711_MS81_SCGE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D039_181105L39_exp180711_MS81_SCGE_AB43.2x36mers.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 D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.1x36mers.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 D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.2x36mers.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 D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.2x36mers.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 D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.1x36mers.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 D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.2x36mers.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 D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D040_181105L40_exp180712_MS63_SCGE-0nM-BE_AB43.2x36mers.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 D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.1x36mers.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 D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.2x36mers.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 D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.2x36mers.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 D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.1x36mers.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 D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.2x36mers.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 D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D041_181105L41_exp180712_MS63_SCGE-10nM-BE_AB43.2x36mers.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 D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.1x36mers.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 D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.2x36mers.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 D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.2x36mers.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 D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.1x36mers.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 D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.2x36mers.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 D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D042_181105L42_exp180712_MS63_SCGE-30nM-BE_AB43.2x36mers.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 D043_181105L43_exp180711_MS1_SCGE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D043_181105L43_exp180711_MS1_SCGE_AB44.1x36mers.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 D043_181105L43_exp180711_MS1_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D043_181105L43_exp180711_MS1_SCGE_AB44.2x36mers.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 D043_181105L43_exp180711_MS1_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D043_181105L43_exp180711_MS1_SCGE_AB44.2x36mers.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 D043_181105L43_exp180711_MS1_SCGE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D043_181105L43_exp180711_MS1_SCGE_AB44.1x36mers.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 D043_181105L43_exp180711_MS1_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D043_181105L43_exp180711_MS1_SCGE_AB44.2x36mers.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 D043_181105L43_exp180711_MS1_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D043_181105L43_exp180711_MS1_SCGE_AB44.2x36mers.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 D044_181105L44_exp180711_MS80_SCGE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D044_181105L44_exp180711_MS80_SCGE_AB44.1x36mers.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 D044_181105L44_exp180711_MS80_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D044_181105L44_exp180711_MS80_SCGE_AB44.2x36mers.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 D044_181105L44_exp180711_MS80_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D044_181105L44_exp180711_MS80_SCGE_AB44.2x36mers.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 D044_181105L44_exp180711_MS80_SCGE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D044_181105L44_exp180711_MS80_SCGE_AB44.1x36mers.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 D044_181105L44_exp180711_MS80_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D044_181105L44_exp180711_MS80_SCGE_AB44.2x36mers.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 D044_181105L44_exp180711_MS80_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D044_181105L44_exp180711_MS80_SCGE_AB44.2x36mers.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 D045_181105L45_exp180711_MS81_SCGE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D045_181105L45_exp180711_MS81_SCGE_AB44.1x36mers.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 D045_181105L45_exp180711_MS81_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D045_181105L45_exp180711_MS81_SCGE_AB44.2x36mers.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 D045_181105L45_exp180711_MS81_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D045_181105L45_exp180711_MS81_SCGE_AB44.2x36mers.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 D045_181105L45_exp180711_MS81_SCGE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D045_181105L45_exp180711_MS81_SCGE_AB44.1x36mers.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 D045_181105L45_exp180711_MS81_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D045_181105L45_exp180711_MS81_SCGE_AB44.2x36mers.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 D045_181105L45_exp180711_MS81_SCGE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D045_181105L45_exp180711_MS81_SCGE_AB44.2x36mers.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 D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.1x36mers.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 D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.2x36mers.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 D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.2x36mers.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 D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.1x36mers.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 D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.2x36mers.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 D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D046_181105L46_exp180712_MS63_SCGE-0nM-BE_AB44.2x36mers.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 D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.1x36mers.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 D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.2x36mers.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 D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.2x36mers.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 D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.1x36mers.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 D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.2x36mers.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 D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D047_181105L47_exp180712_MS63_SCGE-10nM-BE_AB44.2x36mers.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 D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.1x36mers.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 D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.2x36mers.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 D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.2x36mers.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 D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.1x36mers.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 D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.2x36mers.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 D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D048_181105L48_exp180712_MS63_SCGE-30nM-BE_AB44.2x36mers.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 D049_181105L49_exp180711_MS1_SCGE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D049_181105L49_exp180711_MS1_SCGE_AB45.1x36mers.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 D049_181105L49_exp180711_MS1_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D049_181105L49_exp180711_MS1_SCGE_AB45.2x36mers.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 D049_181105L49_exp180711_MS1_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D049_181105L49_exp180711_MS1_SCGE_AB45.2x36mers.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 D049_181105L49_exp180711_MS1_SCGE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D049_181105L49_exp180711_MS1_SCGE_AB45.1x36mers.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 D049_181105L49_exp180711_MS1_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D049_181105L49_exp180711_MS1_SCGE_AB45.2x36mers.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 D049_181105L49_exp180711_MS1_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D049_181105L49_exp180711_MS1_SCGE_AB45.2x36mers.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 D050_181105L50_exp180711_MS80_SCGE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D050_181105L50_exp180711_MS80_SCGE_AB45.1x36mers.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 D050_181105L50_exp180711_MS80_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D050_181105L50_exp180711_MS80_SCGE_AB45.2x36mers.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 D050_181105L50_exp180711_MS80_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D050_181105L50_exp180711_MS80_SCGE_AB45.2x36mers.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 D050_181105L50_exp180711_MS80_SCGE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D050_181105L50_exp180711_MS80_SCGE_AB45.1x36mers.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 D050_181105L50_exp180711_MS80_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D050_181105L50_exp180711_MS80_SCGE_AB45.2x36mers.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 D050_181105L50_exp180711_MS80_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D050_181105L50_exp180711_MS80_SCGE_AB45.2x36mers.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 D051_181105L51_exp180711_MS81_SCGE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D051_181105L51_exp180711_MS81_SCGE_AB45.1x36mers.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 D051_181105L51_exp180711_MS81_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D051_181105L51_exp180711_MS81_SCGE_AB45.2x36mers.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 D051_181105L51_exp180711_MS81_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D051_181105L51_exp180711_MS81_SCGE_AB45.2x36mers.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 D051_181105L51_exp180711_MS81_SCGE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D051_181105L51_exp180711_MS81_SCGE_AB45.1x36mers.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 D051_181105L51_exp180711_MS81_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D051_181105L51_exp180711_MS81_SCGE_AB45.2x36mers.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 D051_181105L51_exp180711_MS81_SCGE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D051_181105L51_exp180711_MS81_SCGE_AB45.2x36mers.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 D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.1x36mers.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 D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.2x36mers.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 D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.2x36mers.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 D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.1x36mers.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 D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.2x36mers.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 D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D052_181105L52_exp180712_MS63_SCGE-0nM-BE_AB45.2x36mers.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 D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.1x36mers.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 D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.2x36mers.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 D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.2x36mers.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 D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.1x36mers.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 D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.2x36mers.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 D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D053_181105L53_exp180712_MS63_SCGE-10nM-BE_AB45.2x36mers.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 D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.1x36mers.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 D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.2x36mers.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 D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.2x36mers.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 D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.1x36mers.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 D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.2x36mers.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 D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D054_181105L54_exp180712_MS63_SCGE-30nM-BE_AB45.2x36mers.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 D055_181105L55_exp180711_MS1_SCGE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D055_181105L55_exp180711_MS1_SCGE_AB46.1x36mers.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 D055_181105L55_exp180711_MS1_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D055_181105L55_exp180711_MS1_SCGE_AB46.2x36mers.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 D055_181105L55_exp180711_MS1_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D055_181105L55_exp180711_MS1_SCGE_AB46.2x36mers.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 D055_181105L55_exp180711_MS1_SCGE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D055_181105L55_exp180711_MS1_SCGE_AB46.1x36mers.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 D055_181105L55_exp180711_MS1_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D055_181105L55_exp180711_MS1_SCGE_AB46.2x36mers.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 D055_181105L55_exp180711_MS1_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D055_181105L55_exp180711_MS1_SCGE_AB46.2x36mers.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 D056_181105L56_exp180711_MS80_SCGE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D056_181105L56_exp180711_MS80_SCGE_AB46.1x36mers.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 D056_181105L56_exp180711_MS80_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D056_181105L56_exp180711_MS80_SCGE_AB46.2x36mers.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 D056_181105L56_exp180711_MS80_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D056_181105L56_exp180711_MS80_SCGE_AB46.2x36mers.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 D056_181105L56_exp180711_MS80_SCGE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D056_181105L56_exp180711_MS80_SCGE_AB46.1x36mers.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 D056_181105L56_exp180711_MS80_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D056_181105L56_exp180711_MS80_SCGE_AB46.2x36mers.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 D056_181105L56_exp180711_MS80_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D056_181105L56_exp180711_MS80_SCGE_AB46.2x36mers.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 D057_181105L57_exp180711_MS81_SCGE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D057_181105L57_exp180711_MS81_SCGE_AB46.1x36mers.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 D057_181105L57_exp180711_MS81_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D057_181105L57_exp180711_MS81_SCGE_AB46.2x36mers.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 D057_181105L57_exp180711_MS81_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D057_181105L57_exp180711_MS81_SCGE_AB46.2x36mers.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 D057_181105L57_exp180711_MS81_SCGE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D057_181105L57_exp180711_MS81_SCGE_AB46.1x36mers.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 D057_181105L57_exp180711_MS81_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D057_181105L57_exp180711_MS81_SCGE_AB46.2x36mers.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 D057_181105L57_exp180711_MS81_SCGE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D057_181105L57_exp180711_MS81_SCGE_AB46.2x36mers.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 D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.1x36mers.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 D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.2x36mers.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 D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.2x36mers.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 D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.1x36mers.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 D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.2x36mers.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 D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D058_181105L58_exp180712_MS63_SCGE-0nM-BE_AB46.2x36mers.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 D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.1x36mers.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 D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.2x36mers.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 D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.2x36mers.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 D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.1x36mers.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 D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.2x36mers.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 D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D059_181105L59_exp180712_MS63_SCGE-10nM-BE_AB46.2x36mers.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 D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.1x36mers.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 D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.2x36mers.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 D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.2x36mers.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 D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.1x36mers.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 D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.2x36mers.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 D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D060_181105L60_exp180712_MS63_SCGE-30nM-BE_AB46.2x36mers.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 D061_181105L61_exp180711_MS1_SCGE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D061_181105L61_exp180711_MS1_SCGE_AB47.1x36mers.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 D061_181105L61_exp180711_MS1_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D061_181105L61_exp180711_MS1_SCGE_AB47.2x36mers.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 D061_181105L61_exp180711_MS1_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D061_181105L61_exp180711_MS1_SCGE_AB47.2x36mers.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 D061_181105L61_exp180711_MS1_SCGE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D061_181105L61_exp180711_MS1_SCGE_AB47.1x36mers.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 D061_181105L61_exp180711_MS1_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D061_181105L61_exp180711_MS1_SCGE_AB47.2x36mers.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 D061_181105L61_exp180711_MS1_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D061_181105L61_exp180711_MS1_SCGE_AB47.2x36mers.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 D062_181105L62_exp180711_MS80_SCGE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D062_181105L62_exp180711_MS80_SCGE_AB47.1x36mers.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 D062_181105L62_exp180711_MS80_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D062_181105L62_exp180711_MS80_SCGE_AB47.2x36mers.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 D062_181105L62_exp180711_MS80_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D062_181105L62_exp180711_MS80_SCGE_AB47.2x36mers.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 D062_181105L62_exp180711_MS80_SCGE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D062_181105L62_exp180711_MS80_SCGE_AB47.1x36mers.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 D062_181105L62_exp180711_MS80_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D062_181105L62_exp180711_MS80_SCGE_AB47.2x36mers.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 D062_181105L62_exp180711_MS80_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D062_181105L62_exp180711_MS80_SCGE_AB47.2x36mers.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 D063_181105L63_exp180711_MS81_SCGE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D063_181105L63_exp180711_MS81_SCGE_AB47.1x36mers.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 D063_181105L63_exp180711_MS81_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D063_181105L63_exp180711_MS81_SCGE_AB47.2x36mers.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 D063_181105L63_exp180711_MS81_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D063_181105L63_exp180711_MS81_SCGE_AB47.2x36mers.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 D063_181105L63_exp180711_MS81_SCGE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D063_181105L63_exp180711_MS81_SCGE_AB47.1x36mers.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 D063_181105L63_exp180711_MS81_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D063_181105L63_exp180711_MS81_SCGE_AB47.2x36mers.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 D063_181105L63_exp180711_MS81_SCGE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D063_181105L63_exp180711_MS81_SCGE_AB47.2x36mers.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 D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.1x36mers.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 D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.2x36mers.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 D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.2x36mers.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 D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.1x36mers.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 D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.2x36mers.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 D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D064_181105L64_exp180712_MS63_SCGE-0nM-BE_AB47.2x36mers.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 D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.1x36mers.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 D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.2x36mers.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 D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.2x36mers.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 D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.1x36mers.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 D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.2x36mers.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 D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D065_181105L65_exp180712_MS63_SCGE-10nM-BE_AB47.2x36mers.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 D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.1x36mers.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 D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.2x36mers.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 D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.2x36mers.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 D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.1x36mers.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 D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.2x36mers.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 D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D066_181105L66_exp180712_MS63_SCGE-30nM-BE_AB47.2x36mers.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 D067_181105L67_exp180711_MS1_SCGE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D067_181105L67_exp180711_MS1_SCGE_AB48.1x36mers.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 D067_181105L67_exp180711_MS1_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D067_181105L67_exp180711_MS1_SCGE_AB48.2x36mers.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 D067_181105L67_exp180711_MS1_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D067_181105L67_exp180711_MS1_SCGE_AB48.2x36mers.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 D067_181105L67_exp180711_MS1_SCGE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D067_181105L67_exp180711_MS1_SCGE_AB48.1x36mers.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 D067_181105L67_exp180711_MS1_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D067_181105L67_exp180711_MS1_SCGE_AB48.2x36mers.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 D067_181105L67_exp180711_MS1_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D067_181105L67_exp180711_MS1_SCGE_AB48.2x36mers.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 D068_181105L68_exp180711_MS80_SCGE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D068_181105L68_exp180711_MS80_SCGE_AB48.1x36mers.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 D068_181105L68_exp180711_MS80_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D068_181105L68_exp180711_MS80_SCGE_AB48.2x36mers.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 D068_181105L68_exp180711_MS80_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D068_181105L68_exp180711_MS80_SCGE_AB48.2x36mers.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 D068_181105L68_exp180711_MS80_SCGE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D068_181105L68_exp180711_MS80_SCGE_AB48.1x36mers.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 D068_181105L68_exp180711_MS80_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D068_181105L68_exp180711_MS80_SCGE_AB48.2x36mers.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 D068_181105L68_exp180711_MS80_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D068_181105L68_exp180711_MS80_SCGE_AB48.2x36mers.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 D069_181105L69_exp180711_MS81_SCGE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D069_181105L69_exp180711_MS81_SCGE_AB48.1x36mers.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 D069_181105L69_exp180711_MS81_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D069_181105L69_exp180711_MS81_SCGE_AB48.2x36mers.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 D069_181105L69_exp180711_MS81_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D069_181105L69_exp180711_MS81_SCGE_AB48.2x36mers.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 D069_181105L69_exp180711_MS81_SCGE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D069_181105L69_exp180711_MS81_SCGE_AB48.1x36mers.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 D069_181105L69_exp180711_MS81_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D069_181105L69_exp180711_MS81_SCGE_AB48.2x36mers.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 D069_181105L69_exp180711_MS81_SCGE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D069_181105L69_exp180711_MS81_SCGE_AB48.2x36mers.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 D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.1x36mers.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 D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.2x36mers.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 D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.2x36mers.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 D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.1x36mers.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 D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.2x36mers.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 D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D070_181105L70_exp180712_MS63_SCGE-0nM-BE_AB48.2x36mers.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 D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.1x36mers.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 D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.2x36mers.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 D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.2x36mers.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 D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.1x36mers.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 D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.2x36mers.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 D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D071_181105L71_exp180712_MS63_SCGE-10nM-BE_AB48.2x36mers.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 D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.1x36mers.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 D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.2x36mers.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 D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.2x36mers.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 D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.1x36mers.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 D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.2x36mers.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 D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-D072_181105L72_exp180712_MS63_SCGE-30nM-BE_AB48.2x36mers.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 E001_200224L63_exp200101_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E001_200224L63_exp200101_MS207_SCD_RAPA-100min_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 E001_200224L63_exp200101_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E001_200224L63_exp200101_MS207_SCD_RAPA-100min_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 E001_200224L63_exp200101_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E001_200224L63_exp200101_MS207_SCD_RAPA-100min_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 E001_200224L63_exp200101_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E001_200224L63_exp200101_MS207_SCD_RAPA-100min_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 E001_200224L63_exp200101_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E001_200224L63_exp200101_MS207_SCD_RAPA-100min_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 E001_200224L63_exp200101_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E001_200224L63_exp200101_MS207_SCD_RAPA-100min_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 E002_200224L64_exp200101_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E002_200224L64_exp200101_MS289_SCD_RAPA-065min_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 E002_200224L64_exp200101_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E002_200224L64_exp200101_MS289_SCD_RAPA-065min_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 E002_200224L64_exp200101_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E002_200224L64_exp200101_MS289_SCD_RAPA-065min_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 E002_200224L64_exp200101_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E002_200224L64_exp200101_MS289_SCD_RAPA-065min_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 E002_200224L64_exp200101_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E002_200224L64_exp200101_MS289_SCD_RAPA-065min_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 E002_200224L64_exp200101_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E002_200224L64_exp200101_MS289_SCD_RAPA-065min_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 E003_200224L65_exp200101_MS281_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E003_200224L65_exp200101_MS281_SCD_RAPA-100min_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 E003_200224L65_exp200101_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E003_200224L65_exp200101_MS281_SCD_RAPA-100min_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 E003_200224L65_exp200101_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E003_200224L65_exp200101_MS281_SCD_RAPA-100min_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 E003_200224L65_exp200101_MS281_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E003_200224L65_exp200101_MS281_SCD_RAPA-100min_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 E003_200224L65_exp200101_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E003_200224L65_exp200101_MS281_SCD_RAPA-100min_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 E003_200224L65_exp200101_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E003_200224L65_exp200101_MS281_SCD_RAPA-100min_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 E004_200224L66_exp200101_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E004_200224L66_exp200101_MS283_SCD_RAPA-100min_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 E004_200224L66_exp200101_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E004_200224L66_exp200101_MS283_SCD_RAPA-100min_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 E004_200224L66_exp200101_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E004_200224L66_exp200101_MS283_SCD_RAPA-100min_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 E004_200224L66_exp200101_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E004_200224L66_exp200101_MS283_SCD_RAPA-100min_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 E004_200224L66_exp200101_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E004_200224L66_exp200101_MS283_SCD_RAPA-100min_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 E004_200224L66_exp200101_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E004_200224L66_exp200101_MS283_SCD_RAPA-100min_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 E005_200224L67_exp200101_MS285_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E005_200224L67_exp200101_MS285_SCD_RAPA-100min_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 E005_200224L67_exp200101_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E005_200224L67_exp200101_MS285_SCD_RAPA-100min_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 E005_200224L67_exp200101_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E005_200224L67_exp200101_MS285_SCD_RAPA-100min_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 E005_200224L67_exp200101_MS285_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E005_200224L67_exp200101_MS285_SCD_RAPA-100min_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 E005_200224L67_exp200101_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E005_200224L67_exp200101_MS285_SCD_RAPA-100min_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 E005_200224L67_exp200101_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E005_200224L67_exp200101_MS285_SCD_RAPA-100min_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 E006_200224L68_exp200101_MS287_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E006_200224L68_exp200101_MS287_SCD_RAPA-100min_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 E006_200224L68_exp200101_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E006_200224L68_exp200101_MS287_SCD_RAPA-100min_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 E006_200224L68_exp200101_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E006_200224L68_exp200101_MS287_SCD_RAPA-100min_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 E006_200224L68_exp200101_MS287_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E006_200224L68_exp200101_MS287_SCD_RAPA-100min_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 E006_200224L68_exp200101_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E006_200224L68_exp200101_MS287_SCD_RAPA-100min_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 E006_200224L68_exp200101_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E006_200224L68_exp200101_MS287_SCD_RAPA-100min_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 E007_200224L69_exp200101_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E007_200224L69_exp200101_MS207_SCD_RAPA-100min_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 E007_200224L69_exp200101_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E007_200224L69_exp200101_MS207_SCD_RAPA-100min_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 E007_200224L69_exp200101_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E007_200224L69_exp200101_MS207_SCD_RAPA-100min_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 E007_200224L69_exp200101_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E007_200224L69_exp200101_MS207_SCD_RAPA-100min_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 E007_200224L69_exp200101_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E007_200224L69_exp200101_MS207_SCD_RAPA-100min_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 E007_200224L69_exp200101_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E007_200224L69_exp200101_MS207_SCD_RAPA-100min_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 E008_200224L70_exp200101_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E008_200224L70_exp200101_MS289_SCD_RAPA-065min_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 E008_200224L70_exp200101_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E008_200224L70_exp200101_MS289_SCD_RAPA-065min_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 E008_200224L70_exp200101_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E008_200224L70_exp200101_MS289_SCD_RAPA-065min_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 E008_200224L70_exp200101_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E008_200224L70_exp200101_MS289_SCD_RAPA-065min_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 E008_200224L70_exp200101_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E008_200224L70_exp200101_MS289_SCD_RAPA-065min_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 E008_200224L70_exp200101_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E008_200224L70_exp200101_MS289_SCD_RAPA-065min_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 E009_200224L71_exp200101_MS282_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E009_200224L71_exp200101_MS282_SCD_RAPA-100min_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 E009_200224L71_exp200101_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E009_200224L71_exp200101_MS282_SCD_RAPA-100min_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 E009_200224L71_exp200101_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E009_200224L71_exp200101_MS282_SCD_RAPA-100min_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 E009_200224L71_exp200101_MS282_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E009_200224L71_exp200101_MS282_SCD_RAPA-100min_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 E009_200224L71_exp200101_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E009_200224L71_exp200101_MS282_SCD_RAPA-100min_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 E009_200224L71_exp200101_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E009_200224L71_exp200101_MS282_SCD_RAPA-100min_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 E010_200224L72_exp200101_MS284_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E010_200224L72_exp200101_MS284_SCD_RAPA-100min_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 E010_200224L72_exp200101_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E010_200224L72_exp200101_MS284_SCD_RAPA-100min_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 E010_200224L72_exp200101_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E010_200224L72_exp200101_MS284_SCD_RAPA-100min_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 E010_200224L72_exp200101_MS284_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E010_200224L72_exp200101_MS284_SCD_RAPA-100min_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 E010_200224L72_exp200101_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E010_200224L72_exp200101_MS284_SCD_RAPA-100min_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 E010_200224L72_exp200101_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E010_200224L72_exp200101_MS284_SCD_RAPA-100min_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 E011_200224L73_exp200101_MS286_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E011_200224L73_exp200101_MS286_SCD_RAPA-100min_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 E011_200224L73_exp200101_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E011_200224L73_exp200101_MS286_SCD_RAPA-100min_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 E011_200224L73_exp200101_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E011_200224L73_exp200101_MS286_SCD_RAPA-100min_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 E011_200224L73_exp200101_MS286_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E011_200224L73_exp200101_MS286_SCD_RAPA-100min_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 E011_200224L73_exp200101_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E011_200224L73_exp200101_MS286_SCD_RAPA-100min_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 E011_200224L73_exp200101_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E011_200224L73_exp200101_MS286_SCD_RAPA-100min_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 E012_200224L74_exp200101_MS288_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E012_200224L74_exp200101_MS288_SCD_RAPA-100min_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 E012_200224L74_exp200101_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E012_200224L74_exp200101_MS288_SCD_RAPA-100min_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 E012_200224L74_exp200101_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E012_200224L74_exp200101_MS288_SCD_RAPA-100min_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 E012_200224L74_exp200101_MS288_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E012_200224L74_exp200101_MS288_SCD_RAPA-100min_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 E012_200224L74_exp200101_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E012_200224L74_exp200101_MS288_SCD_RAPA-100min_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 E012_200224L74_exp200101_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E012_200224L74_exp200101_MS288_SCD_RAPA-100min_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 E013_200201L25_exp200101_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E013_200201L25_exp200101_MS207_SCD_RAPA-100min_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 E013_200201L25_exp200101_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E013_200201L25_exp200101_MS207_SCD_RAPA-100min_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 E013_200201L25_exp200101_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E013_200201L25_exp200101_MS207_SCD_RAPA-100min_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 E013_200201L25_exp200101_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E013_200201L25_exp200101_MS207_SCD_RAPA-100min_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 E013_200201L25_exp200101_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E013_200201L25_exp200101_MS207_SCD_RAPA-100min_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 E013_200201L25_exp200101_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E013_200201L25_exp200101_MS207_SCD_RAPA-100min_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 E014_200201L26_exp200101_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E014_200201L26_exp200101_MS289_SCD_RAPA-065min_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 E014_200201L26_exp200101_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E014_200201L26_exp200101_MS289_SCD_RAPA-065min_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 E014_200201L26_exp200101_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E014_200201L26_exp200101_MS289_SCD_RAPA-065min_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 E014_200201L26_exp200101_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E014_200201L26_exp200101_MS289_SCD_RAPA-065min_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 E014_200201L26_exp200101_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E014_200201L26_exp200101_MS289_SCD_RAPA-065min_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 E014_200201L26_exp200101_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E014_200201L26_exp200101_MS289_SCD_RAPA-065min_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 E015_200201L27_exp200101_MS281_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E015_200201L27_exp200101_MS281_SCD_RAPA-100min_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 E015_200201L27_exp200101_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E015_200201L27_exp200101_MS281_SCD_RAPA-100min_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 E015_200201L27_exp200101_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E015_200201L27_exp200101_MS281_SCD_RAPA-100min_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 E015_200201L27_exp200101_MS281_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E015_200201L27_exp200101_MS281_SCD_RAPA-100min_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 E015_200201L27_exp200101_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E015_200201L27_exp200101_MS281_SCD_RAPA-100min_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 E015_200201L27_exp200101_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E015_200201L27_exp200101_MS281_SCD_RAPA-100min_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 E016_200201L28_exp200101_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E016_200201L28_exp200101_MS283_SCD_RAPA-100min_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 E016_200201L28_exp200101_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E016_200201L28_exp200101_MS283_SCD_RAPA-100min_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 E016_200201L28_exp200101_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E016_200201L28_exp200101_MS283_SCD_RAPA-100min_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 E016_200201L28_exp200101_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E016_200201L28_exp200101_MS283_SCD_RAPA-100min_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 E016_200201L28_exp200101_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E016_200201L28_exp200101_MS283_SCD_RAPA-100min_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 E016_200201L28_exp200101_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E016_200201L28_exp200101_MS283_SCD_RAPA-100min_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 E017_200201L29_exp200101_MS285_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E017_200201L29_exp200101_MS285_SCD_RAPA-100min_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 E017_200201L29_exp200101_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E017_200201L29_exp200101_MS285_SCD_RAPA-100min_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 E017_200201L29_exp200101_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E017_200201L29_exp200101_MS285_SCD_RAPA-100min_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 E017_200201L29_exp200101_MS285_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E017_200201L29_exp200101_MS285_SCD_RAPA-100min_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 E017_200201L29_exp200101_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E017_200201L29_exp200101_MS285_SCD_RAPA-100min_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 E017_200201L29_exp200101_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E017_200201L29_exp200101_MS285_SCD_RAPA-100min_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 E018_200201L30_exp200101_MS287_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E018_200201L30_exp200101_MS287_SCD_RAPA-100min_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 E018_200201L30_exp200101_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E018_200201L30_exp200101_MS287_SCD_RAPA-100min_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 E018_200201L30_exp200101_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E018_200201L30_exp200101_MS287_SCD_RAPA-100min_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 E018_200201L30_exp200101_MS287_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E018_200201L30_exp200101_MS287_SCD_RAPA-100min_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 E018_200201L30_exp200101_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E018_200201L30_exp200101_MS287_SCD_RAPA-100min_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 E018_200201L30_exp200101_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E018_200201L30_exp200101_MS287_SCD_RAPA-100min_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 E019_200201L31_exp200101_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E019_200201L31_exp200101_MS207_SCD_RAPA-100min_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 E019_200201L31_exp200101_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E019_200201L31_exp200101_MS207_SCD_RAPA-100min_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 E019_200201L31_exp200101_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E019_200201L31_exp200101_MS207_SCD_RAPA-100min_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 E019_200201L31_exp200101_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E019_200201L31_exp200101_MS207_SCD_RAPA-100min_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 E019_200201L31_exp200101_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E019_200201L31_exp200101_MS207_SCD_RAPA-100min_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 E019_200201L31_exp200101_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E019_200201L31_exp200101_MS207_SCD_RAPA-100min_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 E020_200201L32_exp200101_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E020_200201L32_exp200101_MS289_SCD_RAPA-065min_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 E020_200201L32_exp200101_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E020_200201L32_exp200101_MS289_SCD_RAPA-065min_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 E020_200201L32_exp200101_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E020_200201L32_exp200101_MS289_SCD_RAPA-065min_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 E020_200201L32_exp200101_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E020_200201L32_exp200101_MS289_SCD_RAPA-065min_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 E020_200201L32_exp200101_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E020_200201L32_exp200101_MS289_SCD_RAPA-065min_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 E020_200201L32_exp200101_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E020_200201L32_exp200101_MS289_SCD_RAPA-065min_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 E021_200201L33_exp200101_MS282_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E021_200201L33_exp200101_MS282_SCD_RAPA-100min_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 E021_200201L33_exp200101_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E021_200201L33_exp200101_MS282_SCD_RAPA-100min_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 E021_200201L33_exp200101_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E021_200201L33_exp200101_MS282_SCD_RAPA-100min_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 E021_200201L33_exp200101_MS282_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E021_200201L33_exp200101_MS282_SCD_RAPA-100min_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 E021_200201L33_exp200101_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E021_200201L33_exp200101_MS282_SCD_RAPA-100min_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 E021_200201L33_exp200101_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E021_200201L33_exp200101_MS282_SCD_RAPA-100min_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 E022_200201L34_exp200101_MS284_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E022_200201L34_exp200101_MS284_SCD_RAPA-100min_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 E022_200201L34_exp200101_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E022_200201L34_exp200101_MS284_SCD_RAPA-100min_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 E022_200201L34_exp200101_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E022_200201L34_exp200101_MS284_SCD_RAPA-100min_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 E022_200201L34_exp200101_MS284_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E022_200201L34_exp200101_MS284_SCD_RAPA-100min_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 E022_200201L34_exp200101_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E022_200201L34_exp200101_MS284_SCD_RAPA-100min_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 E022_200201L34_exp200101_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E022_200201L34_exp200101_MS284_SCD_RAPA-100min_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 E023_200201L35_exp200101_MS286_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E023_200201L35_exp200101_MS286_SCD_RAPA-100min_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 E023_200201L35_exp200101_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E023_200201L35_exp200101_MS286_SCD_RAPA-100min_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 E023_200201L35_exp200101_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E023_200201L35_exp200101_MS286_SCD_RAPA-100min_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 E023_200201L35_exp200101_MS286_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E023_200201L35_exp200101_MS286_SCD_RAPA-100min_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 E023_200201L35_exp200101_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E023_200201L35_exp200101_MS286_SCD_RAPA-100min_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 E023_200201L35_exp200101_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E023_200201L35_exp200101_MS286_SCD_RAPA-100min_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 E024_200201L36_exp200101_MS288_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E024_200201L36_exp200101_MS288_SCD_RAPA-100min_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 E024_200201L36_exp200101_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E024_200201L36_exp200101_MS288_SCD_RAPA-100min_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 E024_200201L36_exp200101_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E024_200201L36_exp200101_MS288_SCD_RAPA-100min_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 E024_200201L36_exp200101_MS288_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E024_200201L36_exp200101_MS288_SCD_RAPA-100min_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 E024_200201L36_exp200101_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E024_200201L36_exp200101_MS288_SCD_RAPA-100min_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 E024_200201L36_exp200101_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E024_200201L36_exp200101_MS288_SCD_RAPA-100min_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 E025_200216L01_exp200112_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E025_200216L01_exp200112_MS207_SCD_RAPA-100min_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 E025_200216L01_exp200112_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E025_200216L01_exp200112_MS207_SCD_RAPA-100min_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 E025_200216L01_exp200112_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E025_200216L01_exp200112_MS207_SCD_RAPA-100min_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 E025_200216L01_exp200112_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E025_200216L01_exp200112_MS207_SCD_RAPA-100min_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 E025_200216L01_exp200112_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E025_200216L01_exp200112_MS207_SCD_RAPA-100min_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 E025_200216L01_exp200112_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E025_200216L01_exp200112_MS207_SCD_RAPA-100min_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 E026_200216L02_exp200112_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E026_200216L02_exp200112_MS289_SCD_RAPA-065min_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 E026_200216L02_exp200112_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E026_200216L02_exp200112_MS289_SCD_RAPA-065min_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 E026_200216L02_exp200112_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E026_200216L02_exp200112_MS289_SCD_RAPA-065min_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 E026_200216L02_exp200112_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E026_200216L02_exp200112_MS289_SCD_RAPA-065min_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 E026_200216L02_exp200112_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E026_200216L02_exp200112_MS289_SCD_RAPA-065min_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 E026_200216L02_exp200112_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E026_200216L02_exp200112_MS289_SCD_RAPA-065min_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 E027_200216L03_exp200112_MS281_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E027_200216L03_exp200112_MS281_SCD_RAPA-100min_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 E027_200216L03_exp200112_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E027_200216L03_exp200112_MS281_SCD_RAPA-100min_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 E027_200216L03_exp200112_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E027_200216L03_exp200112_MS281_SCD_RAPA-100min_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 E027_200216L03_exp200112_MS281_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E027_200216L03_exp200112_MS281_SCD_RAPA-100min_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 E027_200216L03_exp200112_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E027_200216L03_exp200112_MS281_SCD_RAPA-100min_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 E027_200216L03_exp200112_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E027_200216L03_exp200112_MS281_SCD_RAPA-100min_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 E028_200216L04_exp200112_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E028_200216L04_exp200112_MS283_SCD_RAPA-100min_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 E028_200216L04_exp200112_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E028_200216L04_exp200112_MS283_SCD_RAPA-100min_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 E028_200216L04_exp200112_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E028_200216L04_exp200112_MS283_SCD_RAPA-100min_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 E028_200216L04_exp200112_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E028_200216L04_exp200112_MS283_SCD_RAPA-100min_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 E028_200216L04_exp200112_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E028_200216L04_exp200112_MS283_SCD_RAPA-100min_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 E028_200216L04_exp200112_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E028_200216L04_exp200112_MS283_SCD_RAPA-100min_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 E029_200216L05_exp200112_MS285_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E029_200216L05_exp200112_MS285_SCD_RAPA-100min_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 E029_200216L05_exp200112_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E029_200216L05_exp200112_MS285_SCD_RAPA-100min_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 E029_200216L05_exp200112_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E029_200216L05_exp200112_MS285_SCD_RAPA-100min_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 E029_200216L05_exp200112_MS285_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E029_200216L05_exp200112_MS285_SCD_RAPA-100min_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 E029_200216L05_exp200112_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E029_200216L05_exp200112_MS285_SCD_RAPA-100min_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 E029_200216L05_exp200112_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E029_200216L05_exp200112_MS285_SCD_RAPA-100min_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 E030_200216L06_exp200112_MS287_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E030_200216L06_exp200112_MS287_SCD_RAPA-100min_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 E030_200216L06_exp200112_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E030_200216L06_exp200112_MS287_SCD_RAPA-100min_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 E030_200216L06_exp200112_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E030_200216L06_exp200112_MS287_SCD_RAPA-100min_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 E030_200216L06_exp200112_MS287_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E030_200216L06_exp200112_MS287_SCD_RAPA-100min_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 E030_200216L06_exp200112_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E030_200216L06_exp200112_MS287_SCD_RAPA-100min_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 E030_200216L06_exp200112_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E030_200216L06_exp200112_MS287_SCD_RAPA-100min_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 E031_200216L07_exp200108_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E031_200216L07_exp200108_MS207_SCD_RAPA-100min_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 E031_200216L07_exp200108_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E031_200216L07_exp200108_MS207_SCD_RAPA-100min_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 E031_200216L07_exp200108_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E031_200216L07_exp200108_MS207_SCD_RAPA-100min_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 E031_200216L07_exp200108_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E031_200216L07_exp200108_MS207_SCD_RAPA-100min_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 E031_200216L07_exp200108_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E031_200216L07_exp200108_MS207_SCD_RAPA-100min_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 E031_200216L07_exp200108_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E031_200216L07_exp200108_MS207_SCD_RAPA-100min_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 E032_200216L08_exp200108_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E032_200216L08_exp200108_MS289_SCD_RAPA-065min_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 E032_200216L08_exp200108_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E032_200216L08_exp200108_MS289_SCD_RAPA-065min_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 E032_200216L08_exp200108_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E032_200216L08_exp200108_MS289_SCD_RAPA-065min_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 E032_200216L08_exp200108_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E032_200216L08_exp200108_MS289_SCD_RAPA-065min_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 E032_200216L08_exp200108_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E032_200216L08_exp200108_MS289_SCD_RAPA-065min_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 E032_200216L08_exp200108_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E032_200216L08_exp200108_MS289_SCD_RAPA-065min_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 E033_200216L09_exp200108_MS282_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E033_200216L09_exp200108_MS282_SCD_RAPA-100min_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 E033_200216L09_exp200108_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E033_200216L09_exp200108_MS282_SCD_RAPA-100min_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 E033_200216L09_exp200108_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E033_200216L09_exp200108_MS282_SCD_RAPA-100min_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 E033_200216L09_exp200108_MS282_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E033_200216L09_exp200108_MS282_SCD_RAPA-100min_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 E033_200216L09_exp200108_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E033_200216L09_exp200108_MS282_SCD_RAPA-100min_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 E033_200216L09_exp200108_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E033_200216L09_exp200108_MS282_SCD_RAPA-100min_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 E034_200216L10_exp200108_MS284_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E034_200216L10_exp200108_MS284_SCD_RAPA-100min_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 E034_200216L10_exp200108_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E034_200216L10_exp200108_MS284_SCD_RAPA-100min_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 E034_200216L10_exp200108_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E034_200216L10_exp200108_MS284_SCD_RAPA-100min_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 E034_200216L10_exp200108_MS284_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E034_200216L10_exp200108_MS284_SCD_RAPA-100min_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 E034_200216L10_exp200108_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E034_200216L10_exp200108_MS284_SCD_RAPA-100min_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 E034_200216L10_exp200108_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E034_200216L10_exp200108_MS284_SCD_RAPA-100min_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 E035_200216L11_exp200108_MS286_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E035_200216L11_exp200108_MS286_SCD_RAPA-100min_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 E035_200216L11_exp200108_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E035_200216L11_exp200108_MS286_SCD_RAPA-100min_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 E035_200216L11_exp200108_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E035_200216L11_exp200108_MS286_SCD_RAPA-100min_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 E035_200216L11_exp200108_MS286_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E035_200216L11_exp200108_MS286_SCD_RAPA-100min_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 E035_200216L11_exp200108_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E035_200216L11_exp200108_MS286_SCD_RAPA-100min_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 E035_200216L11_exp200108_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E035_200216L11_exp200108_MS286_SCD_RAPA-100min_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 E036_200216L12_exp200108_MS288_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E036_200216L12_exp200108_MS288_SCD_RAPA-100min_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 E036_200216L12_exp200108_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E036_200216L12_exp200108_MS288_SCD_RAPA-100min_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 E036_200216L12_exp200108_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E036_200216L12_exp200108_MS288_SCD_RAPA-100min_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 E036_200216L12_exp200108_MS288_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E036_200216L12_exp200108_MS288_SCD_RAPA-100min_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 E036_200216L12_exp200108_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E036_200216L12_exp200108_MS288_SCD_RAPA-100min_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 E036_200216L12_exp200108_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E036_200216L12_exp200108_MS288_SCD_RAPA-100min_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 E037_200216L25_exp200112_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E037_200216L25_exp200112_MS207_SCD_RAPA-100min_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 E037_200216L25_exp200112_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E037_200216L25_exp200112_MS207_SCD_RAPA-100min_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 E037_200216L25_exp200112_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E037_200216L25_exp200112_MS207_SCD_RAPA-100min_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 E037_200216L25_exp200112_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E037_200216L25_exp200112_MS207_SCD_RAPA-100min_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 E037_200216L25_exp200112_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E037_200216L25_exp200112_MS207_SCD_RAPA-100min_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 E037_200216L25_exp200112_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E037_200216L25_exp200112_MS207_SCD_RAPA-100min_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 E038_200216L26_exp200112_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E038_200216L26_exp200112_MS289_SCD_RAPA-065min_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 E038_200216L26_exp200112_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E038_200216L26_exp200112_MS289_SCD_RAPA-065min_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 E038_200216L26_exp200112_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E038_200216L26_exp200112_MS289_SCD_RAPA-065min_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 E038_200216L26_exp200112_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E038_200216L26_exp200112_MS289_SCD_RAPA-065min_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 E038_200216L26_exp200112_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E038_200216L26_exp200112_MS289_SCD_RAPA-065min_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 E038_200216L26_exp200112_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E038_200216L26_exp200112_MS289_SCD_RAPA-065min_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 E039_200216L27_exp200112_MS281_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E039_200216L27_exp200112_MS281_SCD_RAPA-100min_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 E039_200216L27_exp200112_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E039_200216L27_exp200112_MS281_SCD_RAPA-100min_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 E039_200216L27_exp200112_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E039_200216L27_exp200112_MS281_SCD_RAPA-100min_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 E039_200216L27_exp200112_MS281_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E039_200216L27_exp200112_MS281_SCD_RAPA-100min_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 E039_200216L27_exp200112_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E039_200216L27_exp200112_MS281_SCD_RAPA-100min_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 E039_200216L27_exp200112_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E039_200216L27_exp200112_MS281_SCD_RAPA-100min_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 E040_200216L28_exp200112_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E040_200216L28_exp200112_MS283_SCD_RAPA-100min_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 E040_200216L28_exp200112_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E040_200216L28_exp200112_MS283_SCD_RAPA-100min_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 E040_200216L28_exp200112_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E040_200216L28_exp200112_MS283_SCD_RAPA-100min_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 E040_200216L28_exp200112_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E040_200216L28_exp200112_MS283_SCD_RAPA-100min_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 E040_200216L28_exp200112_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E040_200216L28_exp200112_MS283_SCD_RAPA-100min_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 E040_200216L28_exp200112_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E040_200216L28_exp200112_MS283_SCD_RAPA-100min_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 E041_200216L29_exp200112_MS285_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E041_200216L29_exp200112_MS285_SCD_RAPA-100min_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 E041_200216L29_exp200112_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E041_200216L29_exp200112_MS285_SCD_RAPA-100min_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 E041_200216L29_exp200112_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E041_200216L29_exp200112_MS285_SCD_RAPA-100min_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 E041_200216L29_exp200112_MS285_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E041_200216L29_exp200112_MS285_SCD_RAPA-100min_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 E041_200216L29_exp200112_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E041_200216L29_exp200112_MS285_SCD_RAPA-100min_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 E041_200216L29_exp200112_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E041_200216L29_exp200112_MS285_SCD_RAPA-100min_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 E042_200216L30_exp200112_MS287_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E042_200216L30_exp200112_MS287_SCD_RAPA-100min_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 E042_200216L30_exp200112_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E042_200216L30_exp200112_MS287_SCD_RAPA-100min_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 E042_200216L30_exp200112_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E042_200216L30_exp200112_MS287_SCD_RAPA-100min_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 E042_200216L30_exp200112_MS287_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E042_200216L30_exp200112_MS287_SCD_RAPA-100min_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 E042_200216L30_exp200112_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E042_200216L30_exp200112_MS287_SCD_RAPA-100min_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 E042_200216L30_exp200112_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E042_200216L30_exp200112_MS287_SCD_RAPA-100min_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 E043_200216L31_exp200108_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E043_200216L31_exp200108_MS207_SCD_RAPA-100min_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 E043_200216L31_exp200108_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E043_200216L31_exp200108_MS207_SCD_RAPA-100min_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 E043_200216L31_exp200108_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E043_200216L31_exp200108_MS207_SCD_RAPA-100min_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 E043_200216L31_exp200108_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E043_200216L31_exp200108_MS207_SCD_RAPA-100min_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 E043_200216L31_exp200108_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E043_200216L31_exp200108_MS207_SCD_RAPA-100min_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 E043_200216L31_exp200108_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E043_200216L31_exp200108_MS207_SCD_RAPA-100min_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 E044_200216L32_exp200108_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E044_200216L32_exp200108_MS289_SCD_RAPA-065min_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 E044_200216L32_exp200108_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E044_200216L32_exp200108_MS289_SCD_RAPA-065min_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 E044_200216L32_exp200108_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E044_200216L32_exp200108_MS289_SCD_RAPA-065min_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 E044_200216L32_exp200108_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E044_200216L32_exp200108_MS289_SCD_RAPA-065min_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 E044_200216L32_exp200108_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E044_200216L32_exp200108_MS289_SCD_RAPA-065min_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 E044_200216L32_exp200108_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E044_200216L32_exp200108_MS289_SCD_RAPA-065min_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 E045_200216L33_exp200108_MS282_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E045_200216L33_exp200108_MS282_SCD_RAPA-100min_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 E045_200216L33_exp200108_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E045_200216L33_exp200108_MS282_SCD_RAPA-100min_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 E045_200216L33_exp200108_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E045_200216L33_exp200108_MS282_SCD_RAPA-100min_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 E045_200216L33_exp200108_MS282_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E045_200216L33_exp200108_MS282_SCD_RAPA-100min_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 E045_200216L33_exp200108_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E045_200216L33_exp200108_MS282_SCD_RAPA-100min_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 E045_200216L33_exp200108_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E045_200216L33_exp200108_MS282_SCD_RAPA-100min_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 E046_200216L33_exp200108_MS284_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E046_200216L33_exp200108_MS284_SCD_RAPA-100min_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 E046_200216L33_exp200108_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E046_200216L33_exp200108_MS284_SCD_RAPA-100min_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 E046_200216L33_exp200108_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E046_200216L33_exp200108_MS284_SCD_RAPA-100min_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 E046_200216L33_exp200108_MS284_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E046_200216L33_exp200108_MS284_SCD_RAPA-100min_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 E046_200216L33_exp200108_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E046_200216L33_exp200108_MS284_SCD_RAPA-100min_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 E046_200216L33_exp200108_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E046_200216L33_exp200108_MS284_SCD_RAPA-100min_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 E047_200216L35_exp200108_MS286_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E047_200216L35_exp200108_MS286_SCD_RAPA-100min_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 E047_200216L35_exp200108_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E047_200216L35_exp200108_MS286_SCD_RAPA-100min_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 E047_200216L35_exp200108_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E047_200216L35_exp200108_MS286_SCD_RAPA-100min_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 E047_200216L35_exp200108_MS286_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E047_200216L35_exp200108_MS286_SCD_RAPA-100min_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 E047_200216L35_exp200108_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E047_200216L35_exp200108_MS286_SCD_RAPA-100min_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 E047_200216L35_exp200108_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E047_200216L35_exp200108_MS286_SCD_RAPA-100min_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 E048_200216L36_exp200108_MS288_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E048_200216L36_exp200108_MS288_SCD_RAPA-100min_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 E048_200216L36_exp200108_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E048_200216L36_exp200108_MS288_SCD_RAPA-100min_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 E048_200216L36_exp200108_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E048_200216L36_exp200108_MS288_SCD_RAPA-100min_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 E048_200216L36_exp200108_MS288_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E048_200216L36_exp200108_MS288_SCD_RAPA-100min_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 E048_200216L36_exp200108_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E048_200216L36_exp200108_MS288_SCD_RAPA-100min_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 E048_200216L36_exp200108_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E048_200216L36_exp200108_MS288_SCD_RAPA-100min_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 E049_190722L01_exp190711_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E049_190722L01_exp190711_MS207_SCD_RAPA-100min_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 E049_190722L01_exp190711_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E049_190722L01_exp190711_MS207_SCD_RAPA-100min_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 E049_190722L01_exp190711_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E049_190722L01_exp190711_MS207_SCD_RAPA-100min_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 E049_190722L01_exp190711_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E049_190722L01_exp190711_MS207_SCD_RAPA-100min_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 E049_190722L01_exp190711_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E049_190722L01_exp190711_MS207_SCD_RAPA-100min_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 E049_190722L01_exp190711_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E049_190722L01_exp190711_MS207_SCD_RAPA-100min_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 E050_190722L08_exp190711_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E050_190722L08_exp190711_MS289_SCD_RAPA-065min_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 E050_190722L08_exp190711_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E050_190722L08_exp190711_MS289_SCD_RAPA-065min_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 E050_190722L08_exp190711_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E050_190722L08_exp190711_MS289_SCD_RAPA-065min_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 E050_190722L08_exp190711_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E050_190722L08_exp190711_MS289_SCD_RAPA-065min_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 E050_190722L08_exp190711_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E050_190722L08_exp190711_MS289_SCD_RAPA-065min_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 E050_190722L08_exp190711_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E050_190722L08_exp190711_MS289_SCD_RAPA-065min_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 E051_190722L02_exp190711_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E051_190722L02_exp190711_MS208_SCD_RAPA-100min_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 E051_190722L02_exp190711_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E051_190722L02_exp190711_MS208_SCD_RAPA-100min_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 E051_190722L02_exp190711_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E051_190722L02_exp190711_MS208_SCD_RAPA-100min_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 E051_190722L02_exp190711_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E051_190722L02_exp190711_MS208_SCD_RAPA-100min_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 E051_190722L02_exp190711_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E051_190722L02_exp190711_MS208_SCD_RAPA-100min_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 E051_190722L02_exp190711_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E051_190722L02_exp190711_MS208_SCD_RAPA-100min_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 E052_190722L03_exp190711_MS281_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E052_190722L03_exp190711_MS281_SCD_RAPA-100min_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 E052_190722L03_exp190711_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E052_190722L03_exp190711_MS281_SCD_RAPA-100min_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 E052_190722L03_exp190711_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E052_190722L03_exp190711_MS281_SCD_RAPA-100min_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 E052_190722L03_exp190711_MS281_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E052_190722L03_exp190711_MS281_SCD_RAPA-100min_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 E052_190722L03_exp190711_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E052_190722L03_exp190711_MS281_SCD_RAPA-100min_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 E052_190722L03_exp190711_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E052_190722L03_exp190711_MS281_SCD_RAPA-100min_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 E053_190722L04_exp190711_MS282_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E053_190722L04_exp190711_MS282_SCD_RAPA-100min_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 E053_190722L04_exp190711_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E053_190722L04_exp190711_MS282_SCD_RAPA-100min_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 E053_190722L04_exp190711_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E053_190722L04_exp190711_MS282_SCD_RAPA-100min_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 E053_190722L04_exp190711_MS282_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E053_190722L04_exp190711_MS282_SCD_RAPA-100min_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 E053_190722L04_exp190711_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E053_190722L04_exp190711_MS282_SCD_RAPA-100min_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 E053_190722L04_exp190711_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E053_190722L04_exp190711_MS282_SCD_RAPA-100min_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 E054_190722L05_exp190711_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E054_190722L05_exp190711_MS283_SCD_RAPA-100min_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 E054_190722L05_exp190711_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E054_190722L05_exp190711_MS283_SCD_RAPA-100min_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 E054_190722L05_exp190711_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E054_190722L05_exp190711_MS283_SCD_RAPA-100min_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 E054_190722L05_exp190711_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E054_190722L05_exp190711_MS283_SCD_RAPA-100min_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 E054_190722L05_exp190711_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E054_190722L05_exp190711_MS283_SCD_RAPA-100min_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 E054_190722L05_exp190711_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E054_190722L05_exp190711_MS283_SCD_RAPA-100min_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 E055_190722L06_exp190711_MS284_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E055_190722L06_exp190711_MS284_SCD_RAPA-100min_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 E055_190722L06_exp190711_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E055_190722L06_exp190711_MS284_SCD_RAPA-100min_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 E055_190722L06_exp190711_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E055_190722L06_exp190711_MS284_SCD_RAPA-100min_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 E055_190722L06_exp190711_MS284_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E055_190722L06_exp190711_MS284_SCD_RAPA-100min_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 E055_190722L06_exp190711_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E055_190722L06_exp190711_MS284_SCD_RAPA-100min_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 E055_190722L06_exp190711_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E055_190722L06_exp190711_MS284_SCD_RAPA-100min_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 E056_190722L07_exp190711_MS285_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E056_190722L07_exp190711_MS285_SCD_RAPA-100min_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 E056_190722L07_exp190711_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E056_190722L07_exp190711_MS285_SCD_RAPA-100min_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 E056_190722L07_exp190711_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E056_190722L07_exp190711_MS285_SCD_RAPA-100min_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 E056_190722L07_exp190711_MS285_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E056_190722L07_exp190711_MS285_SCD_RAPA-100min_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 E056_190722L07_exp190711_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E056_190722L07_exp190711_MS285_SCD_RAPA-100min_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 E056_190722L07_exp190711_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E056_190722L07_exp190711_MS285_SCD_RAPA-100min_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 E057_190722L09_exp190712_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E057_190722L09_exp190712_MS207_SCD_RAPA-100min_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 E057_190722L09_exp190712_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E057_190722L09_exp190712_MS207_SCD_RAPA-100min_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 E057_190722L09_exp190712_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E057_190722L09_exp190712_MS207_SCD_RAPA-100min_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 E057_190722L09_exp190712_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E057_190722L09_exp190712_MS207_SCD_RAPA-100min_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 E057_190722L09_exp190712_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E057_190722L09_exp190712_MS207_SCD_RAPA-100min_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 E057_190722L09_exp190712_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E057_190722L09_exp190712_MS207_SCD_RAPA-100min_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 E058_190722L12_exp190712_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E058_190722L12_exp190712_MS289_SCD_RAPA-065min_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 E058_190722L12_exp190712_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E058_190722L12_exp190712_MS289_SCD_RAPA-065min_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 E058_190722L12_exp190712_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E058_190722L12_exp190712_MS289_SCD_RAPA-065min_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 E058_190722L12_exp190712_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E058_190722L12_exp190712_MS289_SCD_RAPA-065min_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 E058_190722L12_exp190712_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E058_190722L12_exp190712_MS289_SCD_RAPA-065min_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 E058_190722L12_exp190712_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E058_190722L12_exp190712_MS289_SCD_RAPA-065min_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 E059_190722L10_exp190712_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E059_190722L10_exp190712_MS208_SCD_RAPA-100min_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 E059_190722L10_exp190712_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E059_190722L10_exp190712_MS208_SCD_RAPA-100min_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 E059_190722L10_exp190712_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E059_190722L10_exp190712_MS208_SCD_RAPA-100min_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 E059_190722L10_exp190712_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E059_190722L10_exp190712_MS208_SCD_RAPA-100min_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 E059_190722L10_exp190712_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E059_190722L10_exp190712_MS208_SCD_RAPA-100min_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 E059_190722L10_exp190712_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E059_190722L10_exp190712_MS208_SCD_RAPA-100min_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 E060_190722L11_exp190712_MS209_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E060_190722L11_exp190712_MS209_SCD_RAPA-100min_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 E060_190722L11_exp190712_MS209_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E060_190722L11_exp190712_MS209_SCD_RAPA-100min_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 E060_190722L11_exp190712_MS209_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E060_190722L11_exp190712_MS209_SCD_RAPA-100min_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 E060_190722L11_exp190712_MS209_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E060_190722L11_exp190712_MS209_SCD_RAPA-100min_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 E060_190722L11_exp190712_MS209_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E060_190722L11_exp190712_MS209_SCD_RAPA-100min_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 E060_190722L11_exp190712_MS209_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E060_190722L11_exp190712_MS209_SCD_RAPA-100min_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 E061_190923L55_exp190712_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E061_190923L55_exp190712_MS283_SCD_RAPA-100min_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 E061_190923L55_exp190712_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E061_190923L55_exp190712_MS283_SCD_RAPA-100min_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 E061_190923L55_exp190712_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E061_190923L55_exp190712_MS283_SCD_RAPA-100min_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 E061_190923L55_exp190712_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E061_190923L55_exp190712_MS283_SCD_RAPA-100min_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 E061_190923L55_exp190712_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E061_190923L55_exp190712_MS283_SCD_RAPA-100min_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 E061_190923L55_exp190712_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E061_190923L55_exp190712_MS283_SCD_RAPA-100min_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 E062_190923L56_exp190712_MS286_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E062_190923L56_exp190712_MS286_SCD_RAPA-100min_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 E062_190923L56_exp190712_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E062_190923L56_exp190712_MS286_SCD_RAPA-100min_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 E062_190923L56_exp190712_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E062_190923L56_exp190712_MS286_SCD_RAPA-100min_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 E062_190923L56_exp190712_MS286_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E062_190923L56_exp190712_MS286_SCD_RAPA-100min_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 E062_190923L56_exp190712_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E062_190923L56_exp190712_MS286_SCD_RAPA-100min_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 E062_190923L56_exp190712_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E062_190923L56_exp190712_MS286_SCD_RAPA-100min_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 E063_190923L57_exp190712_MS287_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E063_190923L57_exp190712_MS287_SCD_RAPA-100min_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 E063_190923L57_exp190712_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E063_190923L57_exp190712_MS287_SCD_RAPA-100min_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 E063_190923L57_exp190712_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E063_190923L57_exp190712_MS287_SCD_RAPA-100min_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 E063_190923L57_exp190712_MS287_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E063_190923L57_exp190712_MS287_SCD_RAPA-100min_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 E063_190923L57_exp190712_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E063_190923L57_exp190712_MS287_SCD_RAPA-100min_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 E063_190923L57_exp190712_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E063_190923L57_exp190712_MS287_SCD_RAPA-100min_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 E064_190923L58_exp190712_MS288_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E064_190923L58_exp190712_MS288_SCD_RAPA-100min_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 E064_190923L58_exp190712_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E064_190923L58_exp190712_MS288_SCD_RAPA-100min_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 E064_190923L58_exp190712_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E064_190923L58_exp190712_MS288_SCD_RAPA-100min_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 E064_190923L58_exp190712_MS288_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E064_190923L58_exp190712_MS288_SCD_RAPA-100min_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 E064_190923L58_exp190712_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E064_190923L58_exp190712_MS288_SCD_RAPA-100min_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 E064_190923L58_exp190712_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E064_190923L58_exp190712_MS288_SCD_RAPA-100min_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 E065_190722L37_exp190711_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E065_190722L37_exp190711_MS207_SCD_RAPA-100min_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 E065_190722L37_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E065_190722L37_exp190711_MS207_SCD_RAPA-100min_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 E065_190722L37_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E065_190722L37_exp190711_MS207_SCD_RAPA-100min_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 E065_190722L37_exp190711_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E065_190722L37_exp190711_MS207_SCD_RAPA-100min_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 E065_190722L37_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E065_190722L37_exp190711_MS207_SCD_RAPA-100min_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 E065_190722L37_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E065_190722L37_exp190711_MS207_SCD_RAPA-100min_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 E066_190722L44_exp190711_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E066_190722L44_exp190711_MS289_SCD_RAPA-065min_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 E066_190722L44_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E066_190722L44_exp190711_MS289_SCD_RAPA-065min_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 E066_190722L44_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E066_190722L44_exp190711_MS289_SCD_RAPA-065min_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 E066_190722L44_exp190711_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E066_190722L44_exp190711_MS289_SCD_RAPA-065min_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 E066_190722L44_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E066_190722L44_exp190711_MS289_SCD_RAPA-065min_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 E066_190722L44_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E066_190722L44_exp190711_MS289_SCD_RAPA-065min_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 E067_190722L38_exp190711_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E067_190722L38_exp190711_MS208_SCD_RAPA-100min_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 E067_190722L38_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E067_190722L38_exp190711_MS208_SCD_RAPA-100min_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 E067_190722L38_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E067_190722L38_exp190711_MS208_SCD_RAPA-100min_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 E067_190722L38_exp190711_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E067_190722L38_exp190711_MS208_SCD_RAPA-100min_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 E067_190722L38_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E067_190722L38_exp190711_MS208_SCD_RAPA-100min_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 E067_190722L38_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E067_190722L38_exp190711_MS208_SCD_RAPA-100min_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 E068_190722L39_exp190711_MS281_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E068_190722L39_exp190711_MS281_SCD_RAPA-100min_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 E068_190722L39_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E068_190722L39_exp190711_MS281_SCD_RAPA-100min_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 E068_190722L39_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E068_190722L39_exp190711_MS281_SCD_RAPA-100min_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 E068_190722L39_exp190711_MS281_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E068_190722L39_exp190711_MS281_SCD_RAPA-100min_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 E068_190722L39_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E068_190722L39_exp190711_MS281_SCD_RAPA-100min_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 E068_190722L39_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E068_190722L39_exp190711_MS281_SCD_RAPA-100min_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 E069_190722L40_exp190711_MS282_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E069_190722L40_exp190711_MS282_SCD_RAPA-100min_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 E069_190722L40_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E069_190722L40_exp190711_MS282_SCD_RAPA-100min_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 E069_190722L40_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E069_190722L40_exp190711_MS282_SCD_RAPA-100min_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 E069_190722L40_exp190711_MS282_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E069_190722L40_exp190711_MS282_SCD_RAPA-100min_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 E069_190722L40_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E069_190722L40_exp190711_MS282_SCD_RAPA-100min_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 E069_190722L40_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E069_190722L40_exp190711_MS282_SCD_RAPA-100min_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 E070_190722L41_exp190711_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E070_190722L41_exp190711_MS283_SCD_RAPA-100min_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 E070_190722L41_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E070_190722L41_exp190711_MS283_SCD_RAPA-100min_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 E070_190722L41_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E070_190722L41_exp190711_MS283_SCD_RAPA-100min_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 E070_190722L41_exp190711_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E070_190722L41_exp190711_MS283_SCD_RAPA-100min_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 E070_190722L41_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E070_190722L41_exp190711_MS283_SCD_RAPA-100min_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 E070_190722L41_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E070_190722L41_exp190711_MS283_SCD_RAPA-100min_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 E071_190722L42_exp190711_MS284_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E071_190722L42_exp190711_MS284_SCD_RAPA-100min_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 E071_190722L42_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E071_190722L42_exp190711_MS284_SCD_RAPA-100min_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 E071_190722L42_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E071_190722L42_exp190711_MS284_SCD_RAPA-100min_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 E071_190722L42_exp190711_MS284_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E071_190722L42_exp190711_MS284_SCD_RAPA-100min_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 E071_190722L42_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E071_190722L42_exp190711_MS284_SCD_RAPA-100min_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 E071_190722L42_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E071_190722L42_exp190711_MS284_SCD_RAPA-100min_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 E072_190722L43_exp190711_MS285_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E072_190722L43_exp190711_MS285_SCD_RAPA-100min_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 E072_190722L43_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E072_190722L43_exp190711_MS285_SCD_RAPA-100min_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 E072_190722L43_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E072_190722L43_exp190711_MS285_SCD_RAPA-100min_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 E072_190722L43_exp190711_MS285_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E072_190722L43_exp190711_MS285_SCD_RAPA-100min_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 E072_190722L43_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E072_190722L43_exp190711_MS285_SCD_RAPA-100min_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 E072_190722L43_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E072_190722L43_exp190711_MS285_SCD_RAPA-100min_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 E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.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 E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.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 E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.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 E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.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 E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.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 E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E073_190729L17_exp190711_MS207_SCD_RAPA-100min_AB01_R.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 E074_190729L49_exp190711_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E074_190729L49_exp190711_MS207_SCD_RAPA-100min_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 E074_190729L49_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E074_190729L49_exp190711_MS207_SCD_RAPA-100min_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 E074_190729L49_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E074_190729L49_exp190711_MS207_SCD_RAPA-100min_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 E074_190729L49_exp190711_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E074_190729L49_exp190711_MS207_SCD_RAPA-100min_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 E074_190729L49_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E074_190729L49_exp190711_MS207_SCD_RAPA-100min_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 E074_190729L49_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E074_190729L49_exp190711_MS207_SCD_RAPA-100min_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 E075_190729L24_exp190711_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E075_190729L24_exp190711_MS289_SCD_RAPA-065min_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 E075_190729L24_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E075_190729L24_exp190711_MS289_SCD_RAPA-065min_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 E075_190729L24_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E075_190729L24_exp190711_MS289_SCD_RAPA-065min_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 E075_190729L24_exp190711_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E075_190729L24_exp190711_MS289_SCD_RAPA-065min_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 E075_190729L24_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E075_190729L24_exp190711_MS289_SCD_RAPA-065min_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 E075_190729L24_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E075_190729L24_exp190711_MS289_SCD_RAPA-065min_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 E076_190729L18_exp190711_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E076_190729L18_exp190711_MS208_SCD_RAPA-100min_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 E076_190729L18_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E076_190729L18_exp190711_MS208_SCD_RAPA-100min_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 E076_190729L18_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E076_190729L18_exp190711_MS208_SCD_RAPA-100min_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 E076_190729L18_exp190711_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E076_190729L18_exp190711_MS208_SCD_RAPA-100min_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 E076_190729L18_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E076_190729L18_exp190711_MS208_SCD_RAPA-100min_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 E076_190729L18_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E076_190729L18_exp190711_MS208_SCD_RAPA-100min_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 E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.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 E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.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 E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.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 E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.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 E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.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 E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E077_190729L50_exp190711_MS208_SCD_RAPA-100min_AB01_R.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 E078_190729L19_exp190711_MS281_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E078_190729L19_exp190711_MS281_SCD_RAPA-100min_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 E078_190729L19_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E078_190729L19_exp190711_MS281_SCD_RAPA-100min_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 E078_190729L19_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E078_190729L19_exp190711_MS281_SCD_RAPA-100min_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 E078_190729L19_exp190711_MS281_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E078_190729L19_exp190711_MS281_SCD_RAPA-100min_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 E078_190729L19_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E078_190729L19_exp190711_MS281_SCD_RAPA-100min_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 E078_190729L19_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E078_190729L19_exp190711_MS281_SCD_RAPA-100min_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 E079_190729L20_exp190711_MS282_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E079_190729L20_exp190711_MS282_SCD_RAPA-100min_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 E079_190729L20_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E079_190729L20_exp190711_MS282_SCD_RAPA-100min_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 E079_190729L20_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E079_190729L20_exp190711_MS282_SCD_RAPA-100min_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 E079_190729L20_exp190711_MS282_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E079_190729L20_exp190711_MS282_SCD_RAPA-100min_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 E079_190729L20_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E079_190729L20_exp190711_MS282_SCD_RAPA-100min_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 E079_190729L20_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E079_190729L20_exp190711_MS282_SCD_RAPA-100min_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 E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.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 E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.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 E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.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 E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.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 E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.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 E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E080_190729L51_exp190711_MS282_SCD_RAPA-100min_AB01_R.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 E081_190729L21_exp190711_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E081_190729L21_exp190711_MS283_SCD_RAPA-100min_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 E081_190729L21_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E081_190729L21_exp190711_MS283_SCD_RAPA-100min_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 E081_190729L21_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E081_190729L21_exp190711_MS283_SCD_RAPA-100min_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 E081_190729L21_exp190711_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E081_190729L21_exp190711_MS283_SCD_RAPA-100min_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 E081_190729L21_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E081_190729L21_exp190711_MS283_SCD_RAPA-100min_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 E081_190729L21_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E081_190729L21_exp190711_MS283_SCD_RAPA-100min_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 E082_190729L22_exp190711_MS284_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E082_190729L22_exp190711_MS284_SCD_RAPA-100min_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 E082_190729L22_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E082_190729L22_exp190711_MS284_SCD_RAPA-100min_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 E082_190729L22_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E082_190729L22_exp190711_MS284_SCD_RAPA-100min_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 E082_190729L22_exp190711_MS284_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E082_190729L22_exp190711_MS284_SCD_RAPA-100min_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 E082_190729L22_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E082_190729L22_exp190711_MS284_SCD_RAPA-100min_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 E082_190729L22_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E082_190729L22_exp190711_MS284_SCD_RAPA-100min_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 E083_190729L23_exp190711_MS285_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E083_190729L23_exp190711_MS285_SCD_RAPA-100min_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 E083_190729L23_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E083_190729L23_exp190711_MS285_SCD_RAPA-100min_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 E083_190729L23_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E083_190729L23_exp190711_MS285_SCD_RAPA-100min_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 E083_190729L23_exp190711_MS285_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E083_190729L23_exp190711_MS285_SCD_RAPA-100min_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 E083_190729L23_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E083_190729L23_exp190711_MS285_SCD_RAPA-100min_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 E083_190729L23_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E083_190729L23_exp190711_MS285_SCD_RAPA-100min_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 E084_190729L25_exp190712_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E084_190729L25_exp190712_MS207_SCD_RAPA-100min_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 E084_190729L25_exp190712_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E084_190729L25_exp190712_MS207_SCD_RAPA-100min_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 E084_190729L25_exp190712_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E084_190729L25_exp190712_MS207_SCD_RAPA-100min_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 E084_190729L25_exp190712_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E084_190729L25_exp190712_MS207_SCD_RAPA-100min_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 E084_190729L25_exp190712_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E084_190729L25_exp190712_MS207_SCD_RAPA-100min_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 E084_190729L25_exp190712_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E084_190729L25_exp190712_MS207_SCD_RAPA-100min_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 E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.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 E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.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 E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.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 E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.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 E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.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 E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E085_190729L52_exp190712_MS207_SCD_RAPA-100min_AB01_R.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 E086_190729L32_exp190712_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E086_190729L32_exp190712_MS289_SCD_RAPA-065min_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 E086_190729L32_exp190712_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E086_190729L32_exp190712_MS289_SCD_RAPA-065min_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 E086_190729L32_exp190712_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E086_190729L32_exp190712_MS289_SCD_RAPA-065min_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 E086_190729L32_exp190712_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E086_190729L32_exp190712_MS289_SCD_RAPA-065min_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 E086_190729L32_exp190712_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E086_190729L32_exp190712_MS289_SCD_RAPA-065min_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 E086_190729L32_exp190712_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E086_190729L32_exp190712_MS289_SCD_RAPA-065min_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 E087_190729L26_exp190712_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E087_190729L26_exp190712_MS208_SCD_RAPA-100min_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 E087_190729L26_exp190712_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E087_190729L26_exp190712_MS208_SCD_RAPA-100min_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 E087_190729L26_exp190712_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E087_190729L26_exp190712_MS208_SCD_RAPA-100min_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 E087_190729L26_exp190712_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E087_190729L26_exp190712_MS208_SCD_RAPA-100min_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 E087_190729L26_exp190712_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E087_190729L26_exp190712_MS208_SCD_RAPA-100min_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 E087_190729L26_exp190712_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E087_190729L26_exp190712_MS208_SCD_RAPA-100min_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 E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.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 E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.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 E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.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 E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.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 E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.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 E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E088_190729L53_exp190712_MS208_SCD_RAPA-100min_AB01_R.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 E089_190729L27_exp190712_MS209_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E089_190729L27_exp190712_MS209_SCD_RAPA-100min_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 E089_190729L27_exp190712_MS209_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E089_190729L27_exp190712_MS209_SCD_RAPA-100min_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 E089_190729L27_exp190712_MS209_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E089_190729L27_exp190712_MS209_SCD_RAPA-100min_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 E089_190729L27_exp190712_MS209_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E089_190729L27_exp190712_MS209_SCD_RAPA-100min_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 E089_190729L27_exp190712_MS209_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E089_190729L27_exp190712_MS209_SCD_RAPA-100min_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 E089_190729L27_exp190712_MS209_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E089_190729L27_exp190712_MS209_SCD_RAPA-100min_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 E090_190729L28_exp190712_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E090_190729L28_exp190712_MS283_SCD_RAPA-100min_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 E090_190729L28_exp190712_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E090_190729L28_exp190712_MS283_SCD_RAPA-100min_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 E090_190729L28_exp190712_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E090_190729L28_exp190712_MS283_SCD_RAPA-100min_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 E090_190729L28_exp190712_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E090_190729L28_exp190712_MS283_SCD_RAPA-100min_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 E090_190729L28_exp190712_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E090_190729L28_exp190712_MS283_SCD_RAPA-100min_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 E090_190729L28_exp190712_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E090_190729L28_exp190712_MS283_SCD_RAPA-100min_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 E091_190729L29_exp190712_MS286_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E091_190729L29_exp190712_MS286_SCD_RAPA-100min_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 E091_190729L29_exp190712_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E091_190729L29_exp190712_MS286_SCD_RAPA-100min_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 E091_190729L29_exp190712_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E091_190729L29_exp190712_MS286_SCD_RAPA-100min_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 E091_190729L29_exp190712_MS286_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E091_190729L29_exp190712_MS286_SCD_RAPA-100min_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 E091_190729L29_exp190712_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E091_190729L29_exp190712_MS286_SCD_RAPA-100min_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 E091_190729L29_exp190712_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E091_190729L29_exp190712_MS286_SCD_RAPA-100min_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 E092_190729L30_exp190712_MS287_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E092_190729L30_exp190712_MS287_SCD_RAPA-100min_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 E092_190729L30_exp190712_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E092_190729L30_exp190712_MS287_SCD_RAPA-100min_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 E092_190729L30_exp190712_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E092_190729L30_exp190712_MS287_SCD_RAPA-100min_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 E092_190729L30_exp190712_MS287_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E092_190729L30_exp190712_MS287_SCD_RAPA-100min_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 E092_190729L30_exp190712_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E092_190729L30_exp190712_MS287_SCD_RAPA-100min_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 E092_190729L30_exp190712_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E092_190729L30_exp190712_MS287_SCD_RAPA-100min_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 E093_190729L31_exp190712_MS288_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E093_190729L31_exp190712_MS288_SCD_RAPA-100min_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 E093_190729L31_exp190712_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E093_190729L31_exp190712_MS288_SCD_RAPA-100min_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 E093_190729L31_exp190712_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E093_190729L31_exp190712_MS288_SCD_RAPA-100min_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 E093_190729L31_exp190712_MS288_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E093_190729L31_exp190712_MS288_SCD_RAPA-100min_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 E093_190729L31_exp190712_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E093_190729L31_exp190712_MS288_SCD_RAPA-100min_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 E093_190729L31_exp190712_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E093_190729L31_exp190712_MS288_SCD_RAPA-100min_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 E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.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 E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.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 E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E094_190729L33_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.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 E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.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 E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E095_190729L40_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.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 E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.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 E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E096_190729L34_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.1x36mers.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 E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.2x36mers.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 E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.2x36mers.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 E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.1x36mers.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 E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.2x36mers.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 E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E097_190729L35_exp190712_MS281_SCD_RAPA-100min_AB04.2x36mers.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 E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.1x36mers.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 E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.2x36mers.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 E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.2x36mers.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 E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.1x36mers.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 E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.2x36mers.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 E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E098_190729L36_exp190712_MS282_SCD_RAPA-100min_AB04.2x36mers.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 E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.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 E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.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 E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E099_190729L37_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.1x36mers.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 E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.2x36mers.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 E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.2x36mers.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 E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.1x36mers.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 E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.2x36mers.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 E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E100_190729L38_exp190712_MS284_SCD_RAPA-100min_AB04.2x36mers.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 E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.1x36mers.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 E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.2x36mers.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 E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.2x36mers.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 E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.1x36mers.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 E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.2x36mers.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 E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E101_190729L39_exp190712_MS285_SCD_RAPA-100min_AB04.2x36mers.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 E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.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 E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.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 E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E102_190729L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.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 E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.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 E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E103_190729L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.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 E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.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 E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E104_190729L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.1x36mers.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 E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.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 E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.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 E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.1x36mers.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 E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.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 E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E105_190729L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.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 E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.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 E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.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 E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E106_190729L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.1x36mers.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 E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.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 E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.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 E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.1x36mers.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 E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.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 E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E107_190729L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.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 E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.1x36mers.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 E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.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 E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.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 E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.1x36mers.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 E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.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 E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E108_190729L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.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 E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.1x36mers.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 E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.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 E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.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 E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.1x36mers.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 E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.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 E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E109_190729L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.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 E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.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 E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.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 E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.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 E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.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 E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.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 E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E110_190729L54_exp190712_MS207_SCD_RAPA-100min_AB04_R.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 E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E111_190729L55_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.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 E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.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 E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.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 E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.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 E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.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 E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E112_190729L56_exp190712_MS283_SCD_RAPA-100min_AB04_R.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 E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E113_190729L58_exp190712_MS208_SCD_RAPA-100min_AB04_R.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 E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.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 E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.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 E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.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 E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.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 E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.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 E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E114_190729L59_exp190712_MS287_SCD_RAPA-100min_AB04_R.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 E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.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 E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.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 E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.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 E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.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 E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.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 E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E115_190729L60_exp190712_MS288_SCD_RAPA-100min_AB04_R.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 E116_191020L01_exp190711_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E116_191020L01_exp190711_MS207_SCD_RAPA-100min_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 E116_191020L01_exp190711_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E116_191020L01_exp190711_MS207_SCD_RAPA-100min_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 E116_191020L01_exp190711_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E116_191020L01_exp190711_MS207_SCD_RAPA-100min_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 E116_191020L01_exp190711_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E116_191020L01_exp190711_MS207_SCD_RAPA-100min_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 E116_191020L01_exp190711_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E116_191020L01_exp190711_MS207_SCD_RAPA-100min_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 E116_191020L01_exp190711_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E116_191020L01_exp190711_MS207_SCD_RAPA-100min_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 E117_191020L08_exp190711_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E117_191020L08_exp190711_MS289_SCD_RAPA-065min_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 E117_191020L08_exp190711_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E117_191020L08_exp190711_MS289_SCD_RAPA-065min_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 E117_191020L08_exp190711_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E117_191020L08_exp190711_MS289_SCD_RAPA-065min_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 E117_191020L08_exp190711_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E117_191020L08_exp190711_MS289_SCD_RAPA-065min_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 E117_191020L08_exp190711_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E117_191020L08_exp190711_MS289_SCD_RAPA-065min_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 E117_191020L08_exp190711_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E117_191020L08_exp190711_MS289_SCD_RAPA-065min_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 E118_191020L02_exp190711_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E118_191020L02_exp190711_MS208_SCD_RAPA-100min_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 E118_191020L02_exp190711_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E118_191020L02_exp190711_MS208_SCD_RAPA-100min_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 E118_191020L02_exp190711_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E118_191020L02_exp190711_MS208_SCD_RAPA-100min_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 E118_191020L02_exp190711_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E118_191020L02_exp190711_MS208_SCD_RAPA-100min_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 E118_191020L02_exp190711_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E118_191020L02_exp190711_MS208_SCD_RAPA-100min_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 E118_191020L02_exp190711_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E118_191020L02_exp190711_MS208_SCD_RAPA-100min_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 E119_191020L03_exp190711_MS281_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E119_191020L03_exp190711_MS281_SCD_RAPA-100min_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 E119_191020L03_exp190711_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E119_191020L03_exp190711_MS281_SCD_RAPA-100min_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 E119_191020L03_exp190711_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E119_191020L03_exp190711_MS281_SCD_RAPA-100min_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 E119_191020L03_exp190711_MS281_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E119_191020L03_exp190711_MS281_SCD_RAPA-100min_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 E119_191020L03_exp190711_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E119_191020L03_exp190711_MS281_SCD_RAPA-100min_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 E119_191020L03_exp190711_MS281_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E119_191020L03_exp190711_MS281_SCD_RAPA-100min_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 E120_191020L04_exp190711_MS282_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E120_191020L04_exp190711_MS282_SCD_RAPA-100min_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 E120_191020L04_exp190711_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E120_191020L04_exp190711_MS282_SCD_RAPA-100min_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 E120_191020L04_exp190711_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E120_191020L04_exp190711_MS282_SCD_RAPA-100min_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 E120_191020L04_exp190711_MS282_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E120_191020L04_exp190711_MS282_SCD_RAPA-100min_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 E120_191020L04_exp190711_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E120_191020L04_exp190711_MS282_SCD_RAPA-100min_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 E120_191020L04_exp190711_MS282_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E120_191020L04_exp190711_MS282_SCD_RAPA-100min_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 E121_191020L04_exp190711_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E121_191020L04_exp190711_MS283_SCD_RAPA-100min_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 E121_191020L04_exp190711_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E121_191020L04_exp190711_MS283_SCD_RAPA-100min_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 E121_191020L04_exp190711_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E121_191020L04_exp190711_MS283_SCD_RAPA-100min_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 E121_191020L04_exp190711_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E121_191020L04_exp190711_MS283_SCD_RAPA-100min_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 E121_191020L04_exp190711_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E121_191020L04_exp190711_MS283_SCD_RAPA-100min_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 E121_191020L04_exp190711_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E121_191020L04_exp190711_MS283_SCD_RAPA-100min_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 E122_191020L06_exp190711_MS284_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E122_191020L06_exp190711_MS284_SCD_RAPA-100min_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 E122_191020L06_exp190711_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E122_191020L06_exp190711_MS284_SCD_RAPA-100min_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 E122_191020L06_exp190711_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E122_191020L06_exp190711_MS284_SCD_RAPA-100min_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 E122_191020L06_exp190711_MS284_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E122_191020L06_exp190711_MS284_SCD_RAPA-100min_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 E122_191020L06_exp190711_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E122_191020L06_exp190711_MS284_SCD_RAPA-100min_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 E122_191020L06_exp190711_MS284_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E122_191020L06_exp190711_MS284_SCD_RAPA-100min_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 E123_191020L07_exp190711_MS285_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E123_191020L07_exp190711_MS285_SCD_RAPA-100min_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 E123_191020L07_exp190711_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E123_191020L07_exp190711_MS285_SCD_RAPA-100min_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 E123_191020L07_exp190711_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E123_191020L07_exp190711_MS285_SCD_RAPA-100min_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 E123_191020L07_exp190711_MS285_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E123_191020L07_exp190711_MS285_SCD_RAPA-100min_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 E123_191020L07_exp190711_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E123_191020L07_exp190711_MS285_SCD_RAPA-100min_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 E123_191020L07_exp190711_MS285_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E123_191020L07_exp190711_MS285_SCD_RAPA-100min_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 E124_191020L09_exp190711_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E124_191020L09_exp190711_MS207_SCD_RAPA-100min_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 E124_191020L09_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E124_191020L09_exp190711_MS207_SCD_RAPA-100min_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 E124_191020L09_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E124_191020L09_exp190711_MS207_SCD_RAPA-100min_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 E124_191020L09_exp190711_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E124_191020L09_exp190711_MS207_SCD_RAPA-100min_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 E124_191020L09_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E124_191020L09_exp190711_MS207_SCD_RAPA-100min_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 E124_191020L09_exp190711_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E124_191020L09_exp190711_MS207_SCD_RAPA-100min_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 E125_191020L16_exp190711_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E125_191020L16_exp190711_MS289_SCD_RAPA-065min_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 E125_191020L16_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E125_191020L16_exp190711_MS289_SCD_RAPA-065min_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 E125_191020L16_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E125_191020L16_exp190711_MS289_SCD_RAPA-065min_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 E125_191020L16_exp190711_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E125_191020L16_exp190711_MS289_SCD_RAPA-065min_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 E125_191020L16_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E125_191020L16_exp190711_MS289_SCD_RAPA-065min_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 E125_191020L16_exp190711_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E125_191020L16_exp190711_MS289_SCD_RAPA-065min_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 E126_191020L10_exp190711_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E126_191020L10_exp190711_MS208_SCD_RAPA-100min_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 E126_191020L10_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E126_191020L10_exp190711_MS208_SCD_RAPA-100min_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 E126_191020L10_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E126_191020L10_exp190711_MS208_SCD_RAPA-100min_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 E126_191020L10_exp190711_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E126_191020L10_exp190711_MS208_SCD_RAPA-100min_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 E126_191020L10_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E126_191020L10_exp190711_MS208_SCD_RAPA-100min_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 E126_191020L10_exp190711_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E126_191020L10_exp190711_MS208_SCD_RAPA-100min_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 E127_191020L11_exp190711_MS281_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E127_191020L11_exp190711_MS281_SCD_RAPA-100min_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 E127_191020L11_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E127_191020L11_exp190711_MS281_SCD_RAPA-100min_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 E127_191020L11_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E127_191020L11_exp190711_MS281_SCD_RAPA-100min_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 E127_191020L11_exp190711_MS281_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E127_191020L11_exp190711_MS281_SCD_RAPA-100min_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 E127_191020L11_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E127_191020L11_exp190711_MS281_SCD_RAPA-100min_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 E127_191020L11_exp190711_MS281_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E127_191020L11_exp190711_MS281_SCD_RAPA-100min_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 E128_191020L12_exp190711_MS282_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E128_191020L12_exp190711_MS282_SCD_RAPA-100min_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 E128_191020L12_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E128_191020L12_exp190711_MS282_SCD_RAPA-100min_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 E128_191020L12_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E128_191020L12_exp190711_MS282_SCD_RAPA-100min_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 E128_191020L12_exp190711_MS282_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E128_191020L12_exp190711_MS282_SCD_RAPA-100min_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 E128_191020L12_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E128_191020L12_exp190711_MS282_SCD_RAPA-100min_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 E128_191020L12_exp190711_MS282_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E128_191020L12_exp190711_MS282_SCD_RAPA-100min_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 E129_191020L13_exp190711_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E129_191020L13_exp190711_MS283_SCD_RAPA-100min_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 E129_191020L13_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E129_191020L13_exp190711_MS283_SCD_RAPA-100min_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 E129_191020L13_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E129_191020L13_exp190711_MS283_SCD_RAPA-100min_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 E129_191020L13_exp190711_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E129_191020L13_exp190711_MS283_SCD_RAPA-100min_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 E129_191020L13_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E129_191020L13_exp190711_MS283_SCD_RAPA-100min_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 E129_191020L13_exp190711_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E129_191020L13_exp190711_MS283_SCD_RAPA-100min_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 E130_191020L14_exp190711_MS284_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E130_191020L14_exp190711_MS284_SCD_RAPA-100min_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 E130_191020L14_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E130_191020L14_exp190711_MS284_SCD_RAPA-100min_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 E130_191020L14_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E130_191020L14_exp190711_MS284_SCD_RAPA-100min_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 E130_191020L14_exp190711_MS284_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E130_191020L14_exp190711_MS284_SCD_RAPA-100min_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 E130_191020L14_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E130_191020L14_exp190711_MS284_SCD_RAPA-100min_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 E130_191020L14_exp190711_MS284_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E130_191020L14_exp190711_MS284_SCD_RAPA-100min_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 E131_191020L15_exp190711_MS285_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E131_191020L15_exp190711_MS285_SCD_RAPA-100min_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 E131_191020L15_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E131_191020L15_exp190711_MS285_SCD_RAPA-100min_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 E131_191020L15_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E131_191020L15_exp190711_MS285_SCD_RAPA-100min_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 E131_191020L15_exp190711_MS285_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E131_191020L15_exp190711_MS285_SCD_RAPA-100min_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 E131_191020L15_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E131_191020L15_exp190711_MS285_SCD_RAPA-100min_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 E131_191020L15_exp190711_MS285_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E131_191020L15_exp190711_MS285_SCD_RAPA-100min_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 E132_191020L17_exp190711_MS207_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E132_191020L17_exp190711_MS207_SCD_RAPA-100min_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 E132_191020L17_exp190711_MS207_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E132_191020L17_exp190711_MS207_SCD_RAPA-100min_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 E132_191020L17_exp190711_MS207_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E132_191020L17_exp190711_MS207_SCD_RAPA-100min_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 E132_191020L17_exp190711_MS207_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E132_191020L17_exp190711_MS207_SCD_RAPA-100min_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 E132_191020L17_exp190711_MS207_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E132_191020L17_exp190711_MS207_SCD_RAPA-100min_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 E132_191020L17_exp190711_MS207_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E132_191020L17_exp190711_MS207_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E133_191020L24_exp190711_MS289_SCD_RAPA-065min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E133_191020L24_exp190711_MS289_SCD_RAPA-065min_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 E133_191020L24_exp190711_MS289_SCD_RAPA-065min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E133_191020L24_exp190711_MS289_SCD_RAPA-065min_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 E133_191020L24_exp190711_MS289_SCD_RAPA-065min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E133_191020L24_exp190711_MS289_SCD_RAPA-065min_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 E133_191020L24_exp190711_MS289_SCD_RAPA-065min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E133_191020L24_exp190711_MS289_SCD_RAPA-065min_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 E133_191020L24_exp190711_MS289_SCD_RAPA-065min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E133_191020L24_exp190711_MS289_SCD_RAPA-065min_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 E133_191020L24_exp190711_MS289_SCD_RAPA-065min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E133_191020L24_exp190711_MS289_SCD_RAPA-065min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E134_191020L18_exp190711_MS208_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E134_191020L18_exp190711_MS208_SCD_RAPA-100min_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 E134_191020L18_exp190711_MS208_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E134_191020L18_exp190711_MS208_SCD_RAPA-100min_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 E134_191020L18_exp190711_MS208_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E134_191020L18_exp190711_MS208_SCD_RAPA-100min_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 E134_191020L18_exp190711_MS208_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E134_191020L18_exp190711_MS208_SCD_RAPA-100min_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 E134_191020L18_exp190711_MS208_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E134_191020L18_exp190711_MS208_SCD_RAPA-100min_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 E134_191020L18_exp190711_MS208_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E134_191020L18_exp190711_MS208_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E135_191020L19_exp190711_MS281_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E135_191020L19_exp190711_MS281_SCD_RAPA-100min_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 E135_191020L19_exp190711_MS281_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E135_191020L19_exp190711_MS281_SCD_RAPA-100min_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 E135_191020L19_exp190711_MS281_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E135_191020L19_exp190711_MS281_SCD_RAPA-100min_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 E135_191020L19_exp190711_MS281_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E135_191020L19_exp190711_MS281_SCD_RAPA-100min_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 E135_191020L19_exp190711_MS281_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E135_191020L19_exp190711_MS281_SCD_RAPA-100min_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 E135_191020L19_exp190711_MS281_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E135_191020L19_exp190711_MS281_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E136_191020L20_exp190711_MS282_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E136_191020L20_exp190711_MS282_SCD_RAPA-100min_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 E136_191020L20_exp190711_MS282_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E136_191020L20_exp190711_MS282_SCD_RAPA-100min_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 E136_191020L20_exp190711_MS282_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E136_191020L20_exp190711_MS282_SCD_RAPA-100min_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 E136_191020L20_exp190711_MS282_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E136_191020L20_exp190711_MS282_SCD_RAPA-100min_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 E136_191020L20_exp190711_MS282_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E136_191020L20_exp190711_MS282_SCD_RAPA-100min_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 E136_191020L20_exp190711_MS282_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E136_191020L20_exp190711_MS282_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E137_191020L21_exp190711_MS283_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E137_191020L21_exp190711_MS283_SCD_RAPA-100min_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 E137_191020L21_exp190711_MS283_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E137_191020L21_exp190711_MS283_SCD_RAPA-100min_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 E137_191020L21_exp190711_MS283_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E137_191020L21_exp190711_MS283_SCD_RAPA-100min_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 E137_191020L21_exp190711_MS283_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E137_191020L21_exp190711_MS283_SCD_RAPA-100min_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 E137_191020L21_exp190711_MS283_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E137_191020L21_exp190711_MS283_SCD_RAPA-100min_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 E137_191020L21_exp190711_MS283_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E137_191020L21_exp190711_MS283_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E138_191020L22_exp190711_MS284_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E138_191020L22_exp190711_MS284_SCD_RAPA-100min_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 E138_191020L22_exp190711_MS284_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E138_191020L22_exp190711_MS284_SCD_RAPA-100min_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 E138_191020L22_exp190711_MS284_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E138_191020L22_exp190711_MS284_SCD_RAPA-100min_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 E138_191020L22_exp190711_MS284_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E138_191020L22_exp190711_MS284_SCD_RAPA-100min_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 E138_191020L22_exp190711_MS284_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E138_191020L22_exp190711_MS284_SCD_RAPA-100min_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 E138_191020L22_exp190711_MS284_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E138_191020L22_exp190711_MS284_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E139_191020L23_exp190711_MS285_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E139_191020L23_exp190711_MS285_SCD_RAPA-100min_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 E139_191020L23_exp190711_MS285_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E139_191020L23_exp190711_MS285_SCD_RAPA-100min_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 E139_191020L23_exp190711_MS285_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E139_191020L23_exp190711_MS285_SCD_RAPA-100min_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 E139_191020L23_exp190711_MS285_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E139_191020L23_exp190711_MS285_SCD_RAPA-100min_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 E139_191020L23_exp190711_MS285_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E139_191020L23_exp190711_MS285_SCD_RAPA-100min_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 E139_191020L23_exp190711_MS285_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E139_191020L23_exp190711_MS285_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.1x36mers.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 E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.2x36mers.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 E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.2x36mers.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 E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.1x36mers.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 E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.2x36mers.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 E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E140_191020L25_exp190711_MS207_SCD_RAPA-100min_AB48.2x36mers.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 E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.1x36mers.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 E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.2x36mers.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 E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.2x36mers.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 E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.1x36mers.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 E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.2x36mers.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 E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E141_191020L32_exp190711_MS289_SCD_RAPA-065min_AB48.2x36mers.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 E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.1x36mers.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 E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.2x36mers.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 E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.2x36mers.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 E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.1x36mers.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 E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.2x36mers.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 E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E142_191020L26_exp190711_MS208_SCD_RAPA-100min_AB48.2x36mers.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 E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.1x36mers.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 E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.2x36mers.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 E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.2x36mers.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 E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.1x36mers.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 E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.2x36mers.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 E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E143_191020L27_exp190711_MS281_SCD_RAPA-100min_AB48.2x36mers.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 E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.1x36mers.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 E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.2x36mers.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 E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.2x36mers.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 E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.1x36mers.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 E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.2x36mers.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 E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E144_191020L28_exp190711_MS282_SCD_RAPA-100min_AB48.2x36mers.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 E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.1x36mers.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 E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.2x36mers.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 E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.2x36mers.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 E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.1x36mers.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 E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.2x36mers.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 E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E145_191020L29_exp190711_MS283_SCD_RAPA-100min_AB48.2x36mers.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 E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.1x36mers.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 E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.2x36mers.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 E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.2x36mers.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 E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.1x36mers.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 E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.2x36mers.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 E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E146_191020L30_exp190711_MS284_SCD_RAPA-100min_AB48.2x36mers.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 E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.1x36mers.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 E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.2x36mers.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 E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.2x36mers.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 E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.1x36mers.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 E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.2x36mers.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 E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E147_191020L31_exp190711_MS285_SCD_RAPA-100min_AB48.2x36mers.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 E148_191015L01_exp190712_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E148_191015L01_exp190712_MS207_SCD_RAPA-100min_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 E148_191015L01_exp190712_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E148_191015L01_exp190712_MS207_SCD_RAPA-100min_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 E148_191015L01_exp190712_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E148_191015L01_exp190712_MS207_SCD_RAPA-100min_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 E148_191015L01_exp190712_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E148_191015L01_exp190712_MS207_SCD_RAPA-100min_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 E148_191015L01_exp190712_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E148_191015L01_exp190712_MS207_SCD_RAPA-100min_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 E148_191015L01_exp190712_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E148_191015L01_exp190712_MS207_SCD_RAPA-100min_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 E149_191015L08_exp190712_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E149_191015L08_exp190712_MS289_SCD_RAPA-065min_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 E149_191015L08_exp190712_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E149_191015L08_exp190712_MS289_SCD_RAPA-065min_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 E149_191015L08_exp190712_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E149_191015L08_exp190712_MS289_SCD_RAPA-065min_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 E149_191015L08_exp190712_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E149_191015L08_exp190712_MS289_SCD_RAPA-065min_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 E149_191015L08_exp190712_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E149_191015L08_exp190712_MS289_SCD_RAPA-065min_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 E149_191015L08_exp190712_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E149_191015L08_exp190712_MS289_SCD_RAPA-065min_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 E150_191015L02_exp190712_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E150_191015L02_exp190712_MS208_SCD_RAPA-100min_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 E150_191015L02_exp190712_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E150_191015L02_exp190712_MS208_SCD_RAPA-100min_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 E150_191015L02_exp190712_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E150_191015L02_exp190712_MS208_SCD_RAPA-100min_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 E150_191015L02_exp190712_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E150_191015L02_exp190712_MS208_SCD_RAPA-100min_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 E150_191015L02_exp190712_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E150_191015L02_exp190712_MS208_SCD_RAPA-100min_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 E150_191015L02_exp190712_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E150_191015L02_exp190712_MS208_SCD_RAPA-100min_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 E151_191015L03_exp190712_MS209_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E151_191015L03_exp190712_MS209_SCD_RAPA-100min_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 E151_191015L03_exp190712_MS209_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E151_191015L03_exp190712_MS209_SCD_RAPA-100min_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 E151_191015L03_exp190712_MS209_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E151_191015L03_exp190712_MS209_SCD_RAPA-100min_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 E151_191015L03_exp190712_MS209_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E151_191015L03_exp190712_MS209_SCD_RAPA-100min_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 E151_191015L03_exp190712_MS209_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E151_191015L03_exp190712_MS209_SCD_RAPA-100min_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 E151_191015L03_exp190712_MS209_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E151_191015L03_exp190712_MS209_SCD_RAPA-100min_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 E152_191015L04_exp190712_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E152_191015L04_exp190712_MS283_SCD_RAPA-100min_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 E152_191015L04_exp190712_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E152_191015L04_exp190712_MS283_SCD_RAPA-100min_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 E152_191015L04_exp190712_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E152_191015L04_exp190712_MS283_SCD_RAPA-100min_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 E152_191015L04_exp190712_MS283_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E152_191015L04_exp190712_MS283_SCD_RAPA-100min_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 E152_191015L04_exp190712_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E152_191015L04_exp190712_MS283_SCD_RAPA-100min_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 E152_191015L04_exp190712_MS283_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E152_191015L04_exp190712_MS283_SCD_RAPA-100min_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 E153_191015L05_exp190712_MS286_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E153_191015L05_exp190712_MS286_SCD_RAPA-100min_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 E153_191015L05_exp190712_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E153_191015L05_exp190712_MS286_SCD_RAPA-100min_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 E153_191015L05_exp190712_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E153_191015L05_exp190712_MS286_SCD_RAPA-100min_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 E153_191015L05_exp190712_MS286_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E153_191015L05_exp190712_MS286_SCD_RAPA-100min_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 E153_191015L05_exp190712_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E153_191015L05_exp190712_MS286_SCD_RAPA-100min_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 E153_191015L05_exp190712_MS286_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E153_191015L05_exp190712_MS286_SCD_RAPA-100min_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 E154_191015L06_exp190712_MS287_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E154_191015L06_exp190712_MS287_SCD_RAPA-100min_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 E154_191015L06_exp190712_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E154_191015L06_exp190712_MS287_SCD_RAPA-100min_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 E154_191015L06_exp190712_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E154_191015L06_exp190712_MS287_SCD_RAPA-100min_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 E154_191015L06_exp190712_MS287_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E154_191015L06_exp190712_MS287_SCD_RAPA-100min_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 E154_191015L06_exp190712_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E154_191015L06_exp190712_MS287_SCD_RAPA-100min_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 E154_191015L06_exp190712_MS287_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E154_191015L06_exp190712_MS287_SCD_RAPA-100min_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 E155_191015L07_exp190712_MS288_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E155_191015L07_exp190712_MS288_SCD_RAPA-100min_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 E155_191015L07_exp190712_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E155_191015L07_exp190712_MS288_SCD_RAPA-100min_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 E155_191015L07_exp190712_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E155_191015L07_exp190712_MS288_SCD_RAPA-100min_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 E155_191015L07_exp190712_MS288_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E155_191015L07_exp190712_MS288_SCD_RAPA-100min_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 E155_191015L07_exp190712_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E155_191015L07_exp190712_MS288_SCD_RAPA-100min_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 E155_191015L07_exp190712_MS288_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E155_191015L07_exp190712_MS288_SCD_RAPA-100min_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 E156_191015L33_exp190712_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E156_191015L33_exp190712_MS207_SCD_RAPA-100min_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 E156_191015L33_exp190712_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E156_191015L33_exp190712_MS207_SCD_RAPA-100min_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 E156_191015L33_exp190712_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E156_191015L33_exp190712_MS207_SCD_RAPA-100min_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 E156_191015L33_exp190712_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E156_191015L33_exp190712_MS207_SCD_RAPA-100min_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 E156_191015L33_exp190712_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E156_191015L33_exp190712_MS207_SCD_RAPA-100min_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 E156_191015L33_exp190712_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E156_191015L33_exp190712_MS207_SCD_RAPA-100min_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 E157_191015L40_exp190712_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E157_191015L40_exp190712_MS289_SCD_RAPA-065min_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 E157_191015L40_exp190712_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E157_191015L40_exp190712_MS289_SCD_RAPA-065min_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 E157_191015L40_exp190712_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E157_191015L40_exp190712_MS289_SCD_RAPA-065min_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 E157_191015L40_exp190712_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E157_191015L40_exp190712_MS289_SCD_RAPA-065min_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 E157_191015L40_exp190712_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E157_191015L40_exp190712_MS289_SCD_RAPA-065min_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 E157_191015L40_exp190712_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E157_191015L40_exp190712_MS289_SCD_RAPA-065min_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 E158_191015L34_exp190712_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E158_191015L34_exp190712_MS208_SCD_RAPA-100min_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 E158_191015L34_exp190712_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E158_191015L34_exp190712_MS208_SCD_RAPA-100min_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 E158_191015L34_exp190712_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E158_191015L34_exp190712_MS208_SCD_RAPA-100min_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 E158_191015L34_exp190712_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E158_191015L34_exp190712_MS208_SCD_RAPA-100min_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 E158_191015L34_exp190712_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E158_191015L34_exp190712_MS208_SCD_RAPA-100min_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 E158_191015L34_exp190712_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E158_191015L34_exp190712_MS208_SCD_RAPA-100min_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 E159_191015L35_exp190712_MS209_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E159_191015L35_exp190712_MS209_SCD_RAPA-100min_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 E159_191015L35_exp190712_MS209_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E159_191015L35_exp190712_MS209_SCD_RAPA-100min_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 E159_191015L35_exp190712_MS209_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E159_191015L35_exp190712_MS209_SCD_RAPA-100min_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 E159_191015L35_exp190712_MS209_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E159_191015L35_exp190712_MS209_SCD_RAPA-100min_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 E159_191015L35_exp190712_MS209_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E159_191015L35_exp190712_MS209_SCD_RAPA-100min_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 E159_191015L35_exp190712_MS209_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E159_191015L35_exp190712_MS209_SCD_RAPA-100min_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 E160_191015L36_exp190712_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E160_191015L36_exp190712_MS283_SCD_RAPA-100min_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 E160_191015L36_exp190712_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E160_191015L36_exp190712_MS283_SCD_RAPA-100min_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 E160_191015L36_exp190712_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E160_191015L36_exp190712_MS283_SCD_RAPA-100min_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 E160_191015L36_exp190712_MS283_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E160_191015L36_exp190712_MS283_SCD_RAPA-100min_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 E160_191015L36_exp190712_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E160_191015L36_exp190712_MS283_SCD_RAPA-100min_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 E160_191015L36_exp190712_MS283_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E160_191015L36_exp190712_MS283_SCD_RAPA-100min_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 E161_191015L37_exp190712_MS286_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E161_191015L37_exp190712_MS286_SCD_RAPA-100min_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 E161_191015L37_exp190712_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E161_191015L37_exp190712_MS286_SCD_RAPA-100min_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 E161_191015L37_exp190712_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E161_191015L37_exp190712_MS286_SCD_RAPA-100min_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 E161_191015L37_exp190712_MS286_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E161_191015L37_exp190712_MS286_SCD_RAPA-100min_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 E161_191015L37_exp190712_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E161_191015L37_exp190712_MS286_SCD_RAPA-100min_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 E161_191015L37_exp190712_MS286_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E161_191015L37_exp190712_MS286_SCD_RAPA-100min_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 E162_191015L38_exp190712_MS287_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E162_191015L38_exp190712_MS287_SCD_RAPA-100min_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 E162_191015L38_exp190712_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E162_191015L38_exp190712_MS287_SCD_RAPA-100min_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 E162_191015L38_exp190712_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E162_191015L38_exp190712_MS287_SCD_RAPA-100min_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 E162_191015L38_exp190712_MS287_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E162_191015L38_exp190712_MS287_SCD_RAPA-100min_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 E162_191015L38_exp190712_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E162_191015L38_exp190712_MS287_SCD_RAPA-100min_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 E162_191015L38_exp190712_MS287_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E162_191015L38_exp190712_MS287_SCD_RAPA-100min_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 E163_191015L39_exp190712_MS288_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E163_191015L39_exp190712_MS288_SCD_RAPA-100min_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 E163_191015L39_exp190712_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E163_191015L39_exp190712_MS288_SCD_RAPA-100min_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 E163_191015L39_exp190712_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E163_191015L39_exp190712_MS288_SCD_RAPA-100min_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 E163_191015L39_exp190712_MS288_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E163_191015L39_exp190712_MS288_SCD_RAPA-100min_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 E163_191015L39_exp190712_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E163_191015L39_exp190712_MS288_SCD_RAPA-100min_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 E163_191015L39_exp190712_MS288_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E163_191015L39_exp190712_MS288_SCD_RAPA-100min_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 E164_191015L09_exp190712_MS207_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E164_191015L09_exp190712_MS207_SCD_RAPA-100min_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 E164_191015L09_exp190712_MS207_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E164_191015L09_exp190712_MS207_SCD_RAPA-100min_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 E164_191015L09_exp190712_MS207_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E164_191015L09_exp190712_MS207_SCD_RAPA-100min_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 E164_191015L09_exp190712_MS207_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E164_191015L09_exp190712_MS207_SCD_RAPA-100min_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 E164_191015L09_exp190712_MS207_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E164_191015L09_exp190712_MS207_SCD_RAPA-100min_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 E164_191015L09_exp190712_MS207_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E164_191015L09_exp190712_MS207_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E165_191015L16_exp190712_MS289_SCD_RAPA-065min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E165_191015L16_exp190712_MS289_SCD_RAPA-065min_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 E165_191015L16_exp190712_MS289_SCD_RAPA-065min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E165_191015L16_exp190712_MS289_SCD_RAPA-065min_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 E165_191015L16_exp190712_MS289_SCD_RAPA-065min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E165_191015L16_exp190712_MS289_SCD_RAPA-065min_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 E165_191015L16_exp190712_MS289_SCD_RAPA-065min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E165_191015L16_exp190712_MS289_SCD_RAPA-065min_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 E165_191015L16_exp190712_MS289_SCD_RAPA-065min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E165_191015L16_exp190712_MS289_SCD_RAPA-065min_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 E165_191015L16_exp190712_MS289_SCD_RAPA-065min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E165_191015L16_exp190712_MS289_SCD_RAPA-065min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E166_191015L10_exp190712_MS208_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E166_191015L10_exp190712_MS208_SCD_RAPA-100min_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 E166_191015L10_exp190712_MS208_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E166_191015L10_exp190712_MS208_SCD_RAPA-100min_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 E166_191015L10_exp190712_MS208_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E166_191015L10_exp190712_MS208_SCD_RAPA-100min_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 E166_191015L10_exp190712_MS208_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E166_191015L10_exp190712_MS208_SCD_RAPA-100min_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 E166_191015L10_exp190712_MS208_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E166_191015L10_exp190712_MS208_SCD_RAPA-100min_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 E166_191015L10_exp190712_MS208_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E166_191015L10_exp190712_MS208_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E167_191015L11_exp190712_MS209_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E167_191015L11_exp190712_MS209_SCD_RAPA-100min_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 E167_191015L11_exp190712_MS209_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E167_191015L11_exp190712_MS209_SCD_RAPA-100min_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 E167_191015L11_exp190712_MS209_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E167_191015L11_exp190712_MS209_SCD_RAPA-100min_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 E167_191015L11_exp190712_MS209_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E167_191015L11_exp190712_MS209_SCD_RAPA-100min_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 E167_191015L11_exp190712_MS209_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E167_191015L11_exp190712_MS209_SCD_RAPA-100min_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 E167_191015L11_exp190712_MS209_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E167_191015L11_exp190712_MS209_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E168_191015L12_exp190712_MS283_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E168_191015L12_exp190712_MS283_SCD_RAPA-100min_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 E168_191015L12_exp190712_MS283_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E168_191015L12_exp190712_MS283_SCD_RAPA-100min_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 E168_191015L12_exp190712_MS283_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E168_191015L12_exp190712_MS283_SCD_RAPA-100min_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 E168_191015L12_exp190712_MS283_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E168_191015L12_exp190712_MS283_SCD_RAPA-100min_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 E168_191015L12_exp190712_MS283_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E168_191015L12_exp190712_MS283_SCD_RAPA-100min_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 E168_191015L12_exp190712_MS283_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E168_191015L12_exp190712_MS283_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E169_191015L13_exp190712_MS286_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E169_191015L13_exp190712_MS286_SCD_RAPA-100min_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 E169_191015L13_exp190712_MS286_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E169_191015L13_exp190712_MS286_SCD_RAPA-100min_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 E169_191015L13_exp190712_MS286_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E169_191015L13_exp190712_MS286_SCD_RAPA-100min_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 E169_191015L13_exp190712_MS286_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E169_191015L13_exp190712_MS286_SCD_RAPA-100min_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 E169_191015L13_exp190712_MS286_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E169_191015L13_exp190712_MS286_SCD_RAPA-100min_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 E169_191015L13_exp190712_MS286_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E169_191015L13_exp190712_MS286_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E170_191015L14_exp190712_MS287_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E170_191015L14_exp190712_MS287_SCD_RAPA-100min_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 E170_191015L14_exp190712_MS287_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E170_191015L14_exp190712_MS287_SCD_RAPA-100min_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 E170_191015L14_exp190712_MS287_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E170_191015L14_exp190712_MS287_SCD_RAPA-100min_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 E170_191015L14_exp190712_MS287_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E170_191015L14_exp190712_MS287_SCD_RAPA-100min_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 E170_191015L14_exp190712_MS287_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E170_191015L14_exp190712_MS287_SCD_RAPA-100min_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 E170_191015L14_exp190712_MS287_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E170_191015L14_exp190712_MS287_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E171_191015L15_exp190712_MS288_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E171_191015L15_exp190712_MS288_SCD_RAPA-100min_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 E171_191015L15_exp190712_MS288_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E171_191015L15_exp190712_MS288_SCD_RAPA-100min_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 E171_191015L15_exp190712_MS288_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E171_191015L15_exp190712_MS288_SCD_RAPA-100min_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 E171_191015L15_exp190712_MS288_SCD_RAPA-100min_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E171_191015L15_exp190712_MS288_SCD_RAPA-100min_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 E171_191015L15_exp190712_MS288_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E171_191015L15_exp190712_MS288_SCD_RAPA-100min_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 E171_191015L15_exp190712_MS288_SCD_RAPA-100min_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E171_191015L15_exp190712_MS288_SCD_RAPA-100min_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
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.1x36mers.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 E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.2x36mers.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 E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.2x36mers.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 E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.1x36mers.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 E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.2x36mers.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 E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E172_191015L17_exp190712_MS207_SCD_RAPA-100min_AB21.2x36mers.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 E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.1x36mers.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 E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.2x36mers.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 E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.2x36mers.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 E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.1x36mers.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 E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.2x36mers.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 E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E173_191015L24_exp190712_MS289_SCD_RAPA-065min_AB21.2x36mers.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 E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.1x36mers.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 E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.2x36mers.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 E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.2x36mers.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 E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.1x36mers.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 E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.2x36mers.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 E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E174_191015L18_exp190712_MS208_SCD_RAPA-100min_AB21.2x36mers.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 E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.1x36mers.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 E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.2x36mers.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 E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.2x36mers.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 E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.1x36mers.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 E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.2x36mers.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 E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E175_191015L19_exp190712_MS209_SCD_RAPA-100min_AB21.2x36mers.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 E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.1x36mers.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 E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.2x36mers.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 E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.2x36mers.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 E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.1x36mers.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 E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.2x36mers.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 E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E176_191015L20_exp190712_MS283_SCD_RAPA-100min_AB21.2x36mers.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 E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.1x36mers.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 E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.2x36mers.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 E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.2x36mers.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 E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.1x36mers.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 E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.2x36mers.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 E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E177_191015L21_exp190712_MS286_SCD_RAPA-100min_AB21.2x36mers.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 E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.1x36mers.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 E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.2x36mers.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 E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.2x36mers.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 E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.1x36mers.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 E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.2x36mers.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 E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E178_191015L22_exp190712_MS287_SCD_RAPA-100min_AB21.2x36mers.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 E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.1x36mers.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 E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.2x36mers.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 E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.2x36mers.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 E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.1x36mers.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 E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.2x36mers.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 E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E179_191015L23_exp190712_MS288_SCD_RAPA-100min_AB21.2x36mers.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 E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.1x36mers.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 E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.2x36mers.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 E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.2x36mers.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 E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.1x36mers.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 E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.2x36mers.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 E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E180_191015L25_exp190712_MS207_SCD_RAPA-100min_AB48.2x36mers.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 E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.1x36mers.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 E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.2x36mers.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 E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.2x36mers.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 E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.1x36mers.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 E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.2x36mers.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 E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E181_191015L32_exp190712_MS289_SCD_RAPA-065min_AB48.2x36mers.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 E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.1x36mers.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 E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.2x36mers.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 E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.2x36mers.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 E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.1x36mers.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 E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.2x36mers.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 E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E182_191015L26_exp190712_MS208_SCD_RAPA-100min_AB48.2x36mers.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 E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.1x36mers.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 E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.2x36mers.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 E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.2x36mers.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 E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.1x36mers.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 E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.2x36mers.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 E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E183_191015L27_exp190712_MS209_SCD_RAPA-100min_AB48.2x36mers.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 E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.1x36mers.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 E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.2x36mers.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 E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.2x36mers.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 E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.1x36mers.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 E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.2x36mers.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 E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E184_191015L28_exp190712_MS283_SCD_RAPA-100min_AB48.2x36mers.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 E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.1x36mers.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 E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.2x36mers.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 E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.2x36mers.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 E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.1x36mers.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 E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.2x36mers.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 E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E185_191015L29_exp190712_MS286_SCD_RAPA-100min_AB48.2x36mers.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 E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.1x36mers.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 E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.2x36mers.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 E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.2x36mers.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 E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.1x36mers.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 E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.2x36mers.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 E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E186_191015L30_exp190712_MS287_SCD_RAPA-100min_AB48.2x36mers.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 E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.1x36mers.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 E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.2x36mers.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 E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.2x36mers.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 E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.1x36mers.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 E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.2x36mers.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 E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E187_191015L31_exp190712_MS288_SCD_RAPA-100min_AB48.2x36mers.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 E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.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 E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.1x36mers.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 E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E188_191015L41_exp190712_MS207_SCD_RAPA-100min_AB04.2x36mers.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 E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.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 E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.1x36mers.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 E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E189_191015L48_exp190712_MS289_SCD_RAPA-065min_AB04.2x36mers.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 E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.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 E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.1x36mers.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 E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E190_191015L42_exp190712_MS208_SCD_RAPA-100min_AB04.2x36mers.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 E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.1x36mers.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 E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.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 E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.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 E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.1x36mers.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 E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.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 E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E191_191015L43_exp190712_MS209_SCD_RAPA-100min_AB04.2x36mers.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 E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.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 E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.1x36mers.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 E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E192_191015L44_exp190712_MS283_SCD_RAPA-100min_AB04.2x36mers.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 E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.1x36mers.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 E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.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 E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.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 E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.1x36mers.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 E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.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 E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E193_191015L45_exp190712_MS286_SCD_RAPA-100min_AB04.2x36mers.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 E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.1x36mers.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 E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.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 E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.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 E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.1x36mers.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 E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.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 E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E194_191015L46_exp190712_MS287_SCD_RAPA-100min_AB04.2x36mers.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 E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.1x36mers.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 E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.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 E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.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 E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.1x36mers.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 E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.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 E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-E195_191015L47_exp190712_MS288_SCD_RAPA-100min_AB04.2x36mers.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 F001_200201L37_exp200120_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F001_200201L37_exp200120_MS207_SCD_RAPA-100min_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 F001_200201L37_exp200120_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F001_200201L37_exp200120_MS207_SCD_RAPA-100min_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 F001_200201L37_exp200120_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F001_200201L37_exp200120_MS207_SCD_RAPA-100min_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 F001_200201L37_exp200120_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F001_200201L37_exp200120_MS207_SCD_RAPA-100min_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 F001_200201L37_exp200120_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F001_200201L37_exp200120_MS207_SCD_RAPA-100min_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 F001_200201L37_exp200120_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F001_200201L37_exp200120_MS207_SCD_RAPA-100min_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 F002_200201L38_exp200120_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F002_200201L38_exp200120_MS289_SCD_RAPA-065min_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 F002_200201L38_exp200120_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F002_200201L38_exp200120_MS289_SCD_RAPA-065min_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 F002_200201L38_exp200120_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F002_200201L38_exp200120_MS289_SCD_RAPA-065min_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 F002_200201L38_exp200120_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F002_200201L38_exp200120_MS289_SCD_RAPA-065min_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 F002_200201L38_exp200120_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F002_200201L38_exp200120_MS289_SCD_RAPA-065min_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 F002_200201L38_exp200120_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F002_200201L38_exp200120_MS289_SCD_RAPA-065min_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 F003_200201L39_exp200120_MS208_SCD_DMSO-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F003_200201L39_exp200120_MS208_SCD_DMSO-100min_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 F003_200201L39_exp200120_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F003_200201L39_exp200120_MS208_SCD_DMSO-100min_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 F003_200201L39_exp200120_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F003_200201L39_exp200120_MS208_SCD_DMSO-100min_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 F003_200201L39_exp200120_MS208_SCD_DMSO-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F003_200201L39_exp200120_MS208_SCD_DMSO-100min_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 F003_200201L39_exp200120_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F003_200201L39_exp200120_MS208_SCD_DMSO-100min_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 F003_200201L39_exp200120_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F003_200201L39_exp200120_MS208_SCD_DMSO-100min_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 F004_200201L40_exp200120_MS208_SCD_RAPA-040min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F004_200201L40_exp200120_MS208_SCD_RAPA-040min_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 F004_200201L40_exp200120_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F004_200201L40_exp200120_MS208_SCD_RAPA-040min_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 F004_200201L40_exp200120_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F004_200201L40_exp200120_MS208_SCD_RAPA-040min_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 F004_200201L40_exp200120_MS208_SCD_RAPA-040min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F004_200201L40_exp200120_MS208_SCD_RAPA-040min_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 F004_200201L40_exp200120_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F004_200201L40_exp200120_MS208_SCD_RAPA-040min_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 F004_200201L40_exp200120_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F004_200201L40_exp200120_MS208_SCD_RAPA-040min_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 F005_200201L41_exp200120_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F005_200201L41_exp200120_MS208_SCD_RAPA-100min_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 F005_200201L41_exp200120_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F005_200201L41_exp200120_MS208_SCD_RAPA-100min_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 F005_200201L41_exp200120_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F005_200201L41_exp200120_MS208_SCD_RAPA-100min_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 F005_200201L41_exp200120_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F005_200201L41_exp200120_MS208_SCD_RAPA-100min_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 F005_200201L41_exp200120_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F005_200201L41_exp200120_MS208_SCD_RAPA-100min_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 F005_200201L41_exp200120_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F005_200201L41_exp200120_MS208_SCD_RAPA-100min_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 F006_200201L42_exp200120_MS208_SCD_RAPA-ON_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F006_200201L42_exp200120_MS208_SCD_RAPA-ON_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 F006_200201L42_exp200120_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F006_200201L42_exp200120_MS208_SCD_RAPA-ON_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 F006_200201L42_exp200120_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F006_200201L42_exp200120_MS208_SCD_RAPA-ON_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 F006_200201L42_exp200120_MS208_SCD_RAPA-ON_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F006_200201L42_exp200120_MS208_SCD_RAPA-ON_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 F006_200201L42_exp200120_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F006_200201L42_exp200120_MS208_SCD_RAPA-ON_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 F006_200201L42_exp200120_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F006_200201L42_exp200120_MS208_SCD_RAPA-ON_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 F007_200224L75_exp200120_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F007_200224L75_exp200120_MS207_SCD_RAPA-100min_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 F007_200224L75_exp200120_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F007_200224L75_exp200120_MS207_SCD_RAPA-100min_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 F007_200224L75_exp200120_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F007_200224L75_exp200120_MS207_SCD_RAPA-100min_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 F007_200224L75_exp200120_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F007_200224L75_exp200120_MS207_SCD_RAPA-100min_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 F007_200224L75_exp200120_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F007_200224L75_exp200120_MS207_SCD_RAPA-100min_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 F007_200224L75_exp200120_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F007_200224L75_exp200120_MS207_SCD_RAPA-100min_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 F008_200224L76_exp200120_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F008_200224L76_exp200120_MS289_SCD_RAPA-065min_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 F008_200224L76_exp200120_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F008_200224L76_exp200120_MS289_SCD_RAPA-065min_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 F008_200224L76_exp200120_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F008_200224L76_exp200120_MS289_SCD_RAPA-065min_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 F008_200224L76_exp200120_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F008_200224L76_exp200120_MS289_SCD_RAPA-065min_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 F008_200224L76_exp200120_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F008_200224L76_exp200120_MS289_SCD_RAPA-065min_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 F008_200224L76_exp200120_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F008_200224L76_exp200120_MS289_SCD_RAPA-065min_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 F009_200224L77_exp200120_MS208_SCD_DMSO-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F009_200224L77_exp200120_MS208_SCD_DMSO-100min_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 F009_200224L77_exp200120_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F009_200224L77_exp200120_MS208_SCD_DMSO-100min_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 F009_200224L77_exp200120_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F009_200224L77_exp200120_MS208_SCD_DMSO-100min_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 F009_200224L77_exp200120_MS208_SCD_DMSO-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F009_200224L77_exp200120_MS208_SCD_DMSO-100min_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 F009_200224L77_exp200120_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F009_200224L77_exp200120_MS208_SCD_DMSO-100min_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 F009_200224L77_exp200120_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F009_200224L77_exp200120_MS208_SCD_DMSO-100min_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 F010_200224L78_exp200120_MS208_SCD_RAPA-040min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F010_200224L78_exp200120_MS208_SCD_RAPA-040min_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 F010_200224L78_exp200120_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F010_200224L78_exp200120_MS208_SCD_RAPA-040min_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 F010_200224L78_exp200120_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F010_200224L78_exp200120_MS208_SCD_RAPA-040min_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 F010_200224L78_exp200120_MS208_SCD_RAPA-040min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F010_200224L78_exp200120_MS208_SCD_RAPA-040min_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 F010_200224L78_exp200120_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F010_200224L78_exp200120_MS208_SCD_RAPA-040min_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 F010_200224L78_exp200120_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F010_200224L78_exp200120_MS208_SCD_RAPA-040min_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 F011_200224L79_exp200120_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F011_200224L79_exp200120_MS208_SCD_RAPA-100min_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 F011_200224L79_exp200120_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F011_200224L79_exp200120_MS208_SCD_RAPA-100min_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 F011_200224L79_exp200120_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F011_200224L79_exp200120_MS208_SCD_RAPA-100min_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 F011_200224L79_exp200120_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F011_200224L79_exp200120_MS208_SCD_RAPA-100min_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 F011_200224L79_exp200120_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F011_200224L79_exp200120_MS208_SCD_RAPA-100min_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 F011_200224L79_exp200120_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F011_200224L79_exp200120_MS208_SCD_RAPA-100min_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 F012_200224L80_exp200120_MS208_SCD_RAPA-ON_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F012_200224L80_exp200120_MS208_SCD_RAPA-ON_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 F012_200224L80_exp200120_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F012_200224L80_exp200120_MS208_SCD_RAPA-ON_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 F012_200224L80_exp200120_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F012_200224L80_exp200120_MS208_SCD_RAPA-ON_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 F012_200224L80_exp200120_MS208_SCD_RAPA-ON_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F012_200224L80_exp200120_MS208_SCD_RAPA-ON_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 F012_200224L80_exp200120_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F012_200224L80_exp200120_MS208_SCD_RAPA-ON_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 F012_200224L80_exp200120_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F012_200224L80_exp200120_MS208_SCD_RAPA-ON_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 F013_200526L55_exp200120_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F013_200526L55_exp200120_MS207_SCD_RAPA-100min_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 F013_200526L55_exp200120_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F013_200526L55_exp200120_MS207_SCD_RAPA-100min_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 F013_200526L55_exp200120_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F013_200526L55_exp200120_MS207_SCD_RAPA-100min_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 F013_200526L55_exp200120_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F013_200526L55_exp200120_MS207_SCD_RAPA-100min_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 F013_200526L55_exp200120_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F013_200526L55_exp200120_MS207_SCD_RAPA-100min_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 F013_200526L55_exp200120_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F013_200526L55_exp200120_MS207_SCD_RAPA-100min_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 F014_200526L56_exp200120_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F014_200526L56_exp200120_MS289_SCD_RAPA-065min_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 F014_200526L56_exp200120_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F014_200526L56_exp200120_MS289_SCD_RAPA-065min_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 F014_200526L56_exp200120_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F014_200526L56_exp200120_MS289_SCD_RAPA-065min_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 F014_200526L56_exp200120_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F014_200526L56_exp200120_MS289_SCD_RAPA-065min_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 F014_200526L56_exp200120_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F014_200526L56_exp200120_MS289_SCD_RAPA-065min_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 F014_200526L56_exp200120_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F014_200526L56_exp200120_MS289_SCD_RAPA-065min_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 F015_200526L57_exp200120_MS208_SCD_DMSO-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F015_200526L57_exp200120_MS208_SCD_DMSO-100min_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 F015_200526L57_exp200120_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F015_200526L57_exp200120_MS208_SCD_DMSO-100min_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 F015_200526L57_exp200120_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F015_200526L57_exp200120_MS208_SCD_DMSO-100min_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 F015_200526L57_exp200120_MS208_SCD_DMSO-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F015_200526L57_exp200120_MS208_SCD_DMSO-100min_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 F015_200526L57_exp200120_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F015_200526L57_exp200120_MS208_SCD_DMSO-100min_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 F015_200526L57_exp200120_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F015_200526L57_exp200120_MS208_SCD_DMSO-100min_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 F016_200526L58_exp200120_MS208_SCD_RAPA-040min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F016_200526L58_exp200120_MS208_SCD_RAPA-040min_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 F016_200526L58_exp200120_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F016_200526L58_exp200120_MS208_SCD_RAPA-040min_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 F016_200526L58_exp200120_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F016_200526L58_exp200120_MS208_SCD_RAPA-040min_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 F016_200526L58_exp200120_MS208_SCD_RAPA-040min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F016_200526L58_exp200120_MS208_SCD_RAPA-040min_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 F016_200526L58_exp200120_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F016_200526L58_exp200120_MS208_SCD_RAPA-040min_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 F016_200526L58_exp200120_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F016_200526L58_exp200120_MS208_SCD_RAPA-040min_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 F017_200526L59_exp200120_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F017_200526L59_exp200120_MS208_SCD_RAPA-100min_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 F017_200526L59_exp200120_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F017_200526L59_exp200120_MS208_SCD_RAPA-100min_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 F017_200526L59_exp200120_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F017_200526L59_exp200120_MS208_SCD_RAPA-100min_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 F017_200526L59_exp200120_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F017_200526L59_exp200120_MS208_SCD_RAPA-100min_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 F017_200526L59_exp200120_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F017_200526L59_exp200120_MS208_SCD_RAPA-100min_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 F017_200526L59_exp200120_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F017_200526L59_exp200120_MS208_SCD_RAPA-100min_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 F018_200526L60_exp200120_MS208_SCD_RAPA-ON_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F018_200526L60_exp200120_MS208_SCD_RAPA-ON_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 F018_200526L60_exp200120_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F018_200526L60_exp200120_MS208_SCD_RAPA-ON_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 F018_200526L60_exp200120_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F018_200526L60_exp200120_MS208_SCD_RAPA-ON_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 F018_200526L60_exp200120_MS208_SCD_RAPA-ON_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F018_200526L60_exp200120_MS208_SCD_RAPA-ON_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 F018_200526L60_exp200120_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F018_200526L60_exp200120_MS208_SCD_RAPA-ON_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 F018_200526L60_exp200120_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F018_200526L60_exp200120_MS208_SCD_RAPA-ON_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 F019_200526L31_exp200120_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F019_200526L31_exp200120_MS207_SCD_RAPA-100min_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 F019_200526L31_exp200120_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F019_200526L31_exp200120_MS207_SCD_RAPA-100min_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 F019_200526L31_exp200120_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F019_200526L31_exp200120_MS207_SCD_RAPA-100min_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 F019_200526L31_exp200120_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F019_200526L31_exp200120_MS207_SCD_RAPA-100min_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 F019_200526L31_exp200120_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F019_200526L31_exp200120_MS207_SCD_RAPA-100min_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 F019_200526L31_exp200120_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F019_200526L31_exp200120_MS207_SCD_RAPA-100min_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 F020_200526L32_exp200120_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F020_200526L32_exp200120_MS289_SCD_RAPA-065min_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 F020_200526L32_exp200120_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F020_200526L32_exp200120_MS289_SCD_RAPA-065min_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 F020_200526L32_exp200120_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F020_200526L32_exp200120_MS289_SCD_RAPA-065min_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 F020_200526L32_exp200120_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F020_200526L32_exp200120_MS289_SCD_RAPA-065min_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 F020_200526L32_exp200120_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F020_200526L32_exp200120_MS289_SCD_RAPA-065min_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 F020_200526L32_exp200120_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F020_200526L32_exp200120_MS289_SCD_RAPA-065min_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 F021_200526L33_exp200120_MS208_SCD_DMSO-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F021_200526L33_exp200120_MS208_SCD_DMSO-100min_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 F021_200526L33_exp200120_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F021_200526L33_exp200120_MS208_SCD_DMSO-100min_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 F021_200526L33_exp200120_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F021_200526L33_exp200120_MS208_SCD_DMSO-100min_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 F021_200526L33_exp200120_MS208_SCD_DMSO-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F021_200526L33_exp200120_MS208_SCD_DMSO-100min_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 F021_200526L33_exp200120_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F021_200526L33_exp200120_MS208_SCD_DMSO-100min_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 F021_200526L33_exp200120_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F021_200526L33_exp200120_MS208_SCD_DMSO-100min_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 F022_200526L34_exp200120_MS208_SCD_RAPA-040min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F022_200526L34_exp200120_MS208_SCD_RAPA-040min_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 F022_200526L34_exp200120_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F022_200526L34_exp200120_MS208_SCD_RAPA-040min_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 F022_200526L34_exp200120_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F022_200526L34_exp200120_MS208_SCD_RAPA-040min_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 F022_200526L34_exp200120_MS208_SCD_RAPA-040min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F022_200526L34_exp200120_MS208_SCD_RAPA-040min_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 F022_200526L34_exp200120_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F022_200526L34_exp200120_MS208_SCD_RAPA-040min_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 F022_200526L34_exp200120_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F022_200526L34_exp200120_MS208_SCD_RAPA-040min_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 F023_200526L35_exp200120_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F023_200526L35_exp200120_MS208_SCD_RAPA-100min_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 F023_200526L35_exp200120_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F023_200526L35_exp200120_MS208_SCD_RAPA-100min_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 F023_200526L35_exp200120_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F023_200526L35_exp200120_MS208_SCD_RAPA-100min_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 F023_200526L35_exp200120_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F023_200526L35_exp200120_MS208_SCD_RAPA-100min_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 F023_200526L35_exp200120_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F023_200526L35_exp200120_MS208_SCD_RAPA-100min_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 F023_200526L35_exp200120_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F023_200526L35_exp200120_MS208_SCD_RAPA-100min_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 F024_200526L36_exp200120_MS208_SCD_RAPA-ON_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F024_200526L36_exp200120_MS208_SCD_RAPA-ON_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 F024_200526L36_exp200120_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F024_200526L36_exp200120_MS208_SCD_RAPA-ON_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 F024_200526L36_exp200120_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F024_200526L36_exp200120_MS208_SCD_RAPA-ON_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 F024_200526L36_exp200120_MS208_SCD_RAPA-ON_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F024_200526L36_exp200120_MS208_SCD_RAPA-ON_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 F024_200526L36_exp200120_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F024_200526L36_exp200120_MS208_SCD_RAPA-ON_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 F024_200526L36_exp200120_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F024_200526L36_exp200120_MS208_SCD_RAPA-ON_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 F025_200216L37_exp200207_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F025_200216L37_exp200207_MS207_SCD_RAPA-100min_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 F025_200216L37_exp200207_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F025_200216L37_exp200207_MS207_SCD_RAPA-100min_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 F025_200216L37_exp200207_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F025_200216L37_exp200207_MS207_SCD_RAPA-100min_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 F025_200216L37_exp200207_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F025_200216L37_exp200207_MS207_SCD_RAPA-100min_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 F025_200216L37_exp200207_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F025_200216L37_exp200207_MS207_SCD_RAPA-100min_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 F025_200216L37_exp200207_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F025_200216L37_exp200207_MS207_SCD_RAPA-100min_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 F026_200216L38_exp200207_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F026_200216L38_exp200207_MS289_SCD_RAPA-065min_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 F026_200216L38_exp200207_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F026_200216L38_exp200207_MS289_SCD_RAPA-065min_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 F026_200216L38_exp200207_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F026_200216L38_exp200207_MS289_SCD_RAPA-065min_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 F026_200216L38_exp200207_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F026_200216L38_exp200207_MS289_SCD_RAPA-065min_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 F026_200216L38_exp200207_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F026_200216L38_exp200207_MS289_SCD_RAPA-065min_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 F026_200216L38_exp200207_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F026_200216L38_exp200207_MS289_SCD_RAPA-065min_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 F027_200216L39_exp200207_MS208_SCD_DMSO-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F027_200216L39_exp200207_MS208_SCD_DMSO-100min_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 F027_200216L39_exp200207_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F027_200216L39_exp200207_MS208_SCD_DMSO-100min_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 F027_200216L39_exp200207_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F027_200216L39_exp200207_MS208_SCD_DMSO-100min_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 F027_200216L39_exp200207_MS208_SCD_DMSO-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F027_200216L39_exp200207_MS208_SCD_DMSO-100min_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 F027_200216L39_exp200207_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F027_200216L39_exp200207_MS208_SCD_DMSO-100min_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 F027_200216L39_exp200207_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F027_200216L39_exp200207_MS208_SCD_DMSO-100min_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 F028_200216L40_exp200207_MS208_SCD_RAPA-040min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F028_200216L40_exp200207_MS208_SCD_RAPA-040min_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 F028_200216L40_exp200207_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F028_200216L40_exp200207_MS208_SCD_RAPA-040min_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 F028_200216L40_exp200207_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F028_200216L40_exp200207_MS208_SCD_RAPA-040min_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 F028_200216L40_exp200207_MS208_SCD_RAPA-040min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F028_200216L40_exp200207_MS208_SCD_RAPA-040min_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 F028_200216L40_exp200207_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F028_200216L40_exp200207_MS208_SCD_RAPA-040min_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 F028_200216L40_exp200207_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F028_200216L40_exp200207_MS208_SCD_RAPA-040min_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 F029_200216L41_exp200207_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F029_200216L41_exp200207_MS208_SCD_RAPA-100min_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 F029_200216L41_exp200207_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F029_200216L41_exp200207_MS208_SCD_RAPA-100min_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 F029_200216L41_exp200207_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F029_200216L41_exp200207_MS208_SCD_RAPA-100min_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 F029_200216L41_exp200207_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F029_200216L41_exp200207_MS208_SCD_RAPA-100min_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 F029_200216L41_exp200207_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F029_200216L41_exp200207_MS208_SCD_RAPA-100min_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 F029_200216L41_exp200207_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F029_200216L41_exp200207_MS208_SCD_RAPA-100min_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 F030_200216L42_exp200207_MS208_SCD_RAPA-ON_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F030_200216L42_exp200207_MS208_SCD_RAPA-ON_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 F030_200216L42_exp200207_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F030_200216L42_exp200207_MS208_SCD_RAPA-ON_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 F030_200216L42_exp200207_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F030_200216L42_exp200207_MS208_SCD_RAPA-ON_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 F030_200216L42_exp200207_MS208_SCD_RAPA-ON_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F030_200216L42_exp200207_MS208_SCD_RAPA-ON_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 F030_200216L42_exp200207_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F030_200216L42_exp200207_MS208_SCD_RAPA-ON_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 F030_200216L42_exp200207_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F030_200216L42_exp200207_MS208_SCD_RAPA-ON_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 F031_200216L13_exp200207_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F031_200216L13_exp200207_MS207_SCD_RAPA-100min_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 F031_200216L13_exp200207_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F031_200216L13_exp200207_MS207_SCD_RAPA-100min_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 F031_200216L13_exp200207_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F031_200216L13_exp200207_MS207_SCD_RAPA-100min_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 F031_200216L13_exp200207_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F031_200216L13_exp200207_MS207_SCD_RAPA-100min_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 F031_200216L13_exp200207_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F031_200216L13_exp200207_MS207_SCD_RAPA-100min_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 F031_200216L13_exp200207_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F031_200216L13_exp200207_MS207_SCD_RAPA-100min_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 F032_200216L14_exp200207_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F032_200216L14_exp200207_MS289_SCD_RAPA-065min_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 F032_200216L14_exp200207_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F032_200216L14_exp200207_MS289_SCD_RAPA-065min_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 F032_200216L14_exp200207_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F032_200216L14_exp200207_MS289_SCD_RAPA-065min_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 F032_200216L14_exp200207_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F032_200216L14_exp200207_MS289_SCD_RAPA-065min_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 F032_200216L14_exp200207_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F032_200216L14_exp200207_MS289_SCD_RAPA-065min_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 F032_200216L14_exp200207_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F032_200216L14_exp200207_MS289_SCD_RAPA-065min_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 F033_200216L15_exp200207_MS208_SCD_DMSO-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F033_200216L15_exp200207_MS208_SCD_DMSO-100min_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 F033_200216L15_exp200207_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F033_200216L15_exp200207_MS208_SCD_DMSO-100min_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 F033_200216L15_exp200207_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F033_200216L15_exp200207_MS208_SCD_DMSO-100min_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 F033_200216L15_exp200207_MS208_SCD_DMSO-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F033_200216L15_exp200207_MS208_SCD_DMSO-100min_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 F033_200216L15_exp200207_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F033_200216L15_exp200207_MS208_SCD_DMSO-100min_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 F033_200216L15_exp200207_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F033_200216L15_exp200207_MS208_SCD_DMSO-100min_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 F034_200216L88_exp200207_MS208_SCD_RAPA-040min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F034_200216L88_exp200207_MS208_SCD_RAPA-040min_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 F034_200216L88_exp200207_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F034_200216L88_exp200207_MS208_SCD_RAPA-040min_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 F034_200216L88_exp200207_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F034_200216L88_exp200207_MS208_SCD_RAPA-040min_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 F034_200216L88_exp200207_MS208_SCD_RAPA-040min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F034_200216L88_exp200207_MS208_SCD_RAPA-040min_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 F034_200216L88_exp200207_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F034_200216L88_exp200207_MS208_SCD_RAPA-040min_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 F034_200216L88_exp200207_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F034_200216L88_exp200207_MS208_SCD_RAPA-040min_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 F035_200216L17_exp200207_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F035_200216L17_exp200207_MS208_SCD_RAPA-100min_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 F035_200216L17_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F035_200216L17_exp200207_MS208_SCD_RAPA-100min_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 F035_200216L17_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F035_200216L17_exp200207_MS208_SCD_RAPA-100min_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 F035_200216L17_exp200207_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F035_200216L17_exp200207_MS208_SCD_RAPA-100min_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 F035_200216L17_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F035_200216L17_exp200207_MS208_SCD_RAPA-100min_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 F035_200216L17_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F035_200216L17_exp200207_MS208_SCD_RAPA-100min_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 F036_200216L18_exp200207_MS208_SCD_RAPA-ON_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F036_200216L18_exp200207_MS208_SCD_RAPA-ON_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 F036_200216L18_exp200207_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F036_200216L18_exp200207_MS208_SCD_RAPA-ON_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 F036_200216L18_exp200207_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F036_200216L18_exp200207_MS208_SCD_RAPA-ON_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 F036_200216L18_exp200207_MS208_SCD_RAPA-ON_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F036_200216L18_exp200207_MS208_SCD_RAPA-ON_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 F036_200216L18_exp200207_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F036_200216L18_exp200207_MS208_SCD_RAPA-ON_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 F036_200216L18_exp200207_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F036_200216L18_exp200207_MS208_SCD_RAPA-ON_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 F037_200216L87_exp200207_MS208_SCD_DMSO-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F037_200216L87_exp200207_MS208_SCD_DMSO-100min_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 F037_200216L87_exp200207_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F037_200216L87_exp200207_MS208_SCD_DMSO-100min_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 F037_200216L87_exp200207_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F037_200216L87_exp200207_MS208_SCD_DMSO-100min_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 F037_200216L87_exp200207_MS208_SCD_DMSO-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F037_200216L87_exp200207_MS208_SCD_DMSO-100min_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 F037_200216L87_exp200207_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F037_200216L87_exp200207_MS208_SCD_DMSO-100min_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 F037_200216L87_exp200207_MS208_SCD_DMSO-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F037_200216L87_exp200207_MS208_SCD_DMSO-100min_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 F038_200216L89_exp200207_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F038_200216L89_exp200207_MS208_SCD_RAPA-100min_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 F038_200216L89_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F038_200216L89_exp200207_MS208_SCD_RAPA-100min_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 F038_200216L89_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F038_200216L89_exp200207_MS208_SCD_RAPA-100min_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 F038_200216L89_exp200207_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F038_200216L89_exp200207_MS208_SCD_RAPA-100min_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 F038_200216L89_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F038_200216L89_exp200207_MS208_SCD_RAPA-100min_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 F038_200216L89_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F038_200216L89_exp200207_MS208_SCD_RAPA-100min_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 F039_200526L67_exp200207_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F039_200526L67_exp200207_MS207_SCD_RAPA-100min_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 F039_200526L67_exp200207_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F039_200526L67_exp200207_MS207_SCD_RAPA-100min_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 F039_200526L67_exp200207_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F039_200526L67_exp200207_MS207_SCD_RAPA-100min_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 F039_200526L67_exp200207_MS207_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F039_200526L67_exp200207_MS207_SCD_RAPA-100min_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 F039_200526L67_exp200207_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F039_200526L67_exp200207_MS207_SCD_RAPA-100min_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 F039_200526L67_exp200207_MS207_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F039_200526L67_exp200207_MS207_SCD_RAPA-100min_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 F040_200526L68_exp200207_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F040_200526L68_exp200207_MS289_SCD_RAPA-065min_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 F040_200526L68_exp200207_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F040_200526L68_exp200207_MS289_SCD_RAPA-065min_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 F040_200526L68_exp200207_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F040_200526L68_exp200207_MS289_SCD_RAPA-065min_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 F040_200526L68_exp200207_MS289_SCD_RAPA-065min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F040_200526L68_exp200207_MS289_SCD_RAPA-065min_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 F040_200526L68_exp200207_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F040_200526L68_exp200207_MS289_SCD_RAPA-065min_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 F040_200526L68_exp200207_MS289_SCD_RAPA-065min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F040_200526L68_exp200207_MS289_SCD_RAPA-065min_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 F041_200526L69_exp200207_MS208_SCD_DMSO-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F041_200526L69_exp200207_MS208_SCD_DMSO-100min_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 F041_200526L69_exp200207_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F041_200526L69_exp200207_MS208_SCD_DMSO-100min_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 F041_200526L69_exp200207_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F041_200526L69_exp200207_MS208_SCD_DMSO-100min_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 F041_200526L69_exp200207_MS208_SCD_DMSO-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F041_200526L69_exp200207_MS208_SCD_DMSO-100min_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 F041_200526L69_exp200207_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F041_200526L69_exp200207_MS208_SCD_DMSO-100min_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 F041_200526L69_exp200207_MS208_SCD_DMSO-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F041_200526L69_exp200207_MS208_SCD_DMSO-100min_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 F042_200526L70_exp200207_MS208_SCD_RAPA-040min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F042_200526L70_exp200207_MS208_SCD_RAPA-040min_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 F042_200526L70_exp200207_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F042_200526L70_exp200207_MS208_SCD_RAPA-040min_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 F042_200526L70_exp200207_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F042_200526L70_exp200207_MS208_SCD_RAPA-040min_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 F042_200526L70_exp200207_MS208_SCD_RAPA-040min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F042_200526L70_exp200207_MS208_SCD_RAPA-040min_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 F042_200526L70_exp200207_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F042_200526L70_exp200207_MS208_SCD_RAPA-040min_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 F042_200526L70_exp200207_MS208_SCD_RAPA-040min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F042_200526L70_exp200207_MS208_SCD_RAPA-040min_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 F043_200526L71_exp200207_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F043_200526L71_exp200207_MS208_SCD_RAPA-100min_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 F043_200526L71_exp200207_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F043_200526L71_exp200207_MS208_SCD_RAPA-100min_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 F043_200526L71_exp200207_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F043_200526L71_exp200207_MS208_SCD_RAPA-100min_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 F043_200526L71_exp200207_MS208_SCD_RAPA-100min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F043_200526L71_exp200207_MS208_SCD_RAPA-100min_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 F043_200526L71_exp200207_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F043_200526L71_exp200207_MS208_SCD_RAPA-100min_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 F043_200526L71_exp200207_MS208_SCD_RAPA-100min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F043_200526L71_exp200207_MS208_SCD_RAPA-100min_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 F044_200526L72_exp200207_MS208_SCD_RAPA-ON_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F044_200526L72_exp200207_MS208_SCD_RAPA-ON_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 F044_200526L72_exp200207_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F044_200526L72_exp200207_MS208_SCD_RAPA-ON_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 F044_200526L72_exp200207_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F044_200526L72_exp200207_MS208_SCD_RAPA-ON_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 F044_200526L72_exp200207_MS208_SCD_RAPA-ON_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F044_200526L72_exp200207_MS208_SCD_RAPA-ON_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 F044_200526L72_exp200207_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F044_200526L72_exp200207_MS208_SCD_RAPA-ON_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 F044_200526L72_exp200207_MS208_SCD_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F044_200526L72_exp200207_MS208_SCD_RAPA-ON_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 F045_200526L43_exp200207_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F045_200526L43_exp200207_MS207_SCD_RAPA-100min_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 F045_200526L43_exp200207_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F045_200526L43_exp200207_MS207_SCD_RAPA-100min_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 F045_200526L43_exp200207_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F045_200526L43_exp200207_MS207_SCD_RAPA-100min_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 F045_200526L43_exp200207_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F045_200526L43_exp200207_MS207_SCD_RAPA-100min_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 F045_200526L43_exp200207_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F045_200526L43_exp200207_MS207_SCD_RAPA-100min_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 F045_200526L43_exp200207_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F045_200526L43_exp200207_MS207_SCD_RAPA-100min_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 F046_200526L44_exp200207_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F046_200526L44_exp200207_MS289_SCD_RAPA-065min_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 F046_200526L44_exp200207_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F046_200526L44_exp200207_MS289_SCD_RAPA-065min_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 F046_200526L44_exp200207_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F046_200526L44_exp200207_MS289_SCD_RAPA-065min_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 F046_200526L44_exp200207_MS289_SCD_RAPA-065min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F046_200526L44_exp200207_MS289_SCD_RAPA-065min_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 F046_200526L44_exp200207_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F046_200526L44_exp200207_MS289_SCD_RAPA-065min_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 F046_200526L44_exp200207_MS289_SCD_RAPA-065min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F046_200526L44_exp200207_MS289_SCD_RAPA-065min_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 F047_200526L45_exp200207_MS208_SCD_DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F047_200526L45_exp200207_MS208_SCD_DMSO_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 F047_200526L45_exp200207_MS208_SCD_DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F047_200526L45_exp200207_MS208_SCD_DMSO_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 F047_200526L45_exp200207_MS208_SCD_DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F047_200526L45_exp200207_MS208_SCD_DMSO_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 F047_200526L45_exp200207_MS208_SCD_DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F047_200526L45_exp200207_MS208_SCD_DMSO_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 F047_200526L45_exp200207_MS208_SCD_DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F047_200526L45_exp200207_MS208_SCD_DMSO_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 F047_200526L45_exp200207_MS208_SCD_DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F047_200526L45_exp200207_MS208_SCD_DMSO_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 F048_200526L46_exp200207_MS208_SCD_RAPA-040min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F048_200526L46_exp200207_MS208_SCD_RAPA-040min_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 F048_200526L46_exp200207_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F048_200526L46_exp200207_MS208_SCD_RAPA-040min_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 F048_200526L46_exp200207_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F048_200526L46_exp200207_MS208_SCD_RAPA-040min_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 F048_200526L46_exp200207_MS208_SCD_RAPA-040min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F048_200526L46_exp200207_MS208_SCD_RAPA-040min_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 F048_200526L46_exp200207_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F048_200526L46_exp200207_MS208_SCD_RAPA-040min_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 F048_200526L46_exp200207_MS208_SCD_RAPA-040min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F048_200526L46_exp200207_MS208_SCD_RAPA-040min_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 F049_200526L47_exp200207_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F049_200526L47_exp200207_MS208_SCD_RAPA-100min_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 F049_200526L47_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F049_200526L47_exp200207_MS208_SCD_RAPA-100min_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 F049_200526L47_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F049_200526L47_exp200207_MS208_SCD_RAPA-100min_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 F049_200526L47_exp200207_MS208_SCD_RAPA-100min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F049_200526L47_exp200207_MS208_SCD_RAPA-100min_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 F049_200526L47_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F049_200526L47_exp200207_MS208_SCD_RAPA-100min_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 F049_200526L47_exp200207_MS208_SCD_RAPA-100min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F049_200526L47_exp200207_MS208_SCD_RAPA-100min_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 F050_200526L48_exp200207_MS208_SCD_RAPA-ON_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F050_200526L48_exp200207_MS208_SCD_RAPA-ON_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 F050_200526L48_exp200207_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F050_200526L48_exp200207_MS208_SCD_RAPA-ON_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 F050_200526L48_exp200207_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F050_200526L48_exp200207_MS208_SCD_RAPA-ON_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 F050_200526L48_exp200207_MS208_SCD_RAPA-ON_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-F050_200526L48_exp200207_MS208_SCD_RAPA-ON_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 F050_200526L48_exp200207_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F050_200526L48_exp200207_MS208_SCD_RAPA-ON_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 F050_200526L48_exp200207_MS208_SCD_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-F050_200526L48_exp200207_MS208_SCD_RAPA-ON_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 G001_200808L01_exp200802_MS207_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G001_200808L01_exp200802_MS207_SCD_RAPA-40min_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 G001_200808L01_exp200802_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G001_200808L01_exp200802_MS207_SCD_RAPA-40min_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 G001_200808L01_exp200802_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G001_200808L01_exp200802_MS207_SCD_RAPA-40min_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 G001_200808L01_exp200802_MS207_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G001_200808L01_exp200802_MS207_SCD_RAPA-40min_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 G001_200808L01_exp200802_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G001_200808L01_exp200802_MS207_SCD_RAPA-40min_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 G001_200808L01_exp200802_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G001_200808L01_exp200802_MS207_SCD_RAPA-40min_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 G002_200808L02_exp200802_MS208_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G002_200808L02_exp200802_MS208_SCD_RAPA-40min_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 G002_200808L02_exp200802_MS208_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G002_200808L02_exp200802_MS208_SCD_RAPA-40min_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 G002_200808L02_exp200802_MS208_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G002_200808L02_exp200802_MS208_SCD_RAPA-40min_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 G002_200808L02_exp200802_MS208_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G002_200808L02_exp200802_MS208_SCD_RAPA-40min_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 G002_200808L02_exp200802_MS208_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G002_200808L02_exp200802_MS208_SCD_RAPA-40min_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 G002_200808L02_exp200802_MS208_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G002_200808L02_exp200802_MS208_SCD_RAPA-40min_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 G003_200808L03_exp200802_MS209_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G003_200808L03_exp200802_MS209_SCD_RAPA-40min_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 G003_200808L03_exp200802_MS209_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G003_200808L03_exp200802_MS209_SCD_RAPA-40min_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 G003_200808L03_exp200802_MS209_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G003_200808L03_exp200802_MS209_SCD_RAPA-40min_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 G003_200808L03_exp200802_MS209_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G003_200808L03_exp200802_MS209_SCD_RAPA-40min_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 G003_200808L03_exp200802_MS209_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G003_200808L03_exp200802_MS209_SCD_RAPA-40min_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 G003_200808L03_exp200802_MS209_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G003_200808L03_exp200802_MS209_SCD_RAPA-40min_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 G004_200808L04_exp200802_MS282_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G004_200808L04_exp200802_MS282_SCD_RAPA-40min_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 G004_200808L04_exp200802_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G004_200808L04_exp200802_MS282_SCD_RAPA-40min_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 G004_200808L04_exp200802_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G004_200808L04_exp200802_MS282_SCD_RAPA-40min_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 G004_200808L04_exp200802_MS282_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G004_200808L04_exp200802_MS282_SCD_RAPA-40min_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 G004_200808L04_exp200802_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G004_200808L04_exp200802_MS282_SCD_RAPA-40min_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 G004_200808L04_exp200802_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G004_200808L04_exp200802_MS282_SCD_RAPA-40min_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 G005_200808L05_exp200802_MS295_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G005_200808L05_exp200802_MS295_SCD_RAPA-40min_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 G005_200808L05_exp200802_MS295_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G005_200808L05_exp200802_MS295_SCD_RAPA-40min_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 G005_200808L05_exp200802_MS295_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G005_200808L05_exp200802_MS295_SCD_RAPA-40min_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 G005_200808L05_exp200802_MS295_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G005_200808L05_exp200802_MS295_SCD_RAPA-40min_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 G005_200808L05_exp200802_MS295_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G005_200808L05_exp200802_MS295_SCD_RAPA-40min_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 G005_200808L05_exp200802_MS295_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G005_200808L05_exp200802_MS295_SCD_RAPA-40min_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 G006_200808L06_exp200802_MS289_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G006_200808L06_exp200802_MS289_SCD_RAPA-65min_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 G006_200808L06_exp200802_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G006_200808L06_exp200802_MS289_SCD_RAPA-65min_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 G006_200808L06_exp200802_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G006_200808L06_exp200802_MS289_SCD_RAPA-65min_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 G006_200808L06_exp200802_MS289_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G006_200808L06_exp200802_MS289_SCD_RAPA-65min_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 G006_200808L06_exp200802_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G006_200808L06_exp200802_MS289_SCD_RAPA-65min_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 G006_200808L06_exp200802_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G006_200808L06_exp200802_MS289_SCD_RAPA-65min_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 G007_200808L07_exp200803_MS207_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G007_200808L07_exp200803_MS207_SCD_RAPA-40min_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 G007_200808L07_exp200803_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G007_200808L07_exp200803_MS207_SCD_RAPA-40min_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 G007_200808L07_exp200803_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G007_200808L07_exp200803_MS207_SCD_RAPA-40min_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 G007_200808L07_exp200803_MS207_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G007_200808L07_exp200803_MS207_SCD_RAPA-40min_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 G007_200808L07_exp200803_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G007_200808L07_exp200803_MS207_SCD_RAPA-40min_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 G007_200808L07_exp200803_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G007_200808L07_exp200803_MS207_SCD_RAPA-40min_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 G008_200808L08_exp200803_MS281_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G008_200808L08_exp200803_MS281_SCD_RAPA-40min_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 G008_200808L08_exp200803_MS281_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G008_200808L08_exp200803_MS281_SCD_RAPA-40min_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 G008_200808L08_exp200803_MS281_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G008_200808L08_exp200803_MS281_SCD_RAPA-40min_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 G008_200808L08_exp200803_MS281_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G008_200808L08_exp200803_MS281_SCD_RAPA-40min_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 G008_200808L08_exp200803_MS281_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G008_200808L08_exp200803_MS281_SCD_RAPA-40min_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 G008_200808L08_exp200803_MS281_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G008_200808L08_exp200803_MS281_SCD_RAPA-40min_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 G009_200808L09_exp200803_MS282_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G009_200808L09_exp200803_MS282_SCD_RAPA-40min_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 G009_200808L09_exp200803_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G009_200808L09_exp200803_MS282_SCD_RAPA-40min_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 G009_200808L09_exp200803_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G009_200808L09_exp200803_MS282_SCD_RAPA-40min_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 G009_200808L09_exp200803_MS282_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G009_200808L09_exp200803_MS282_SCD_RAPA-40min_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 G009_200808L09_exp200803_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G009_200808L09_exp200803_MS282_SCD_RAPA-40min_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 G009_200808L09_exp200803_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G009_200808L09_exp200803_MS282_SCD_RAPA-40min_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 G010_200808L10_exp200803_MS294_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G010_200808L10_exp200803_MS294_SCD_RAPA-40min_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 G010_200808L10_exp200803_MS294_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G010_200808L10_exp200803_MS294_SCD_RAPA-40min_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 G010_200808L10_exp200803_MS294_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G010_200808L10_exp200803_MS294_SCD_RAPA-40min_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 G010_200808L10_exp200803_MS294_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G010_200808L10_exp200803_MS294_SCD_RAPA-40min_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 G010_200808L10_exp200803_MS294_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G010_200808L10_exp200803_MS294_SCD_RAPA-40min_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 G010_200808L10_exp200803_MS294_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G010_200808L10_exp200803_MS294_SCD_RAPA-40min_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 G011_200808L11_exp200803_MS299_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G011_200808L11_exp200803_MS299_SCD_RAPA-40min_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 G011_200808L11_exp200803_MS299_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G011_200808L11_exp200803_MS299_SCD_RAPA-40min_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 G011_200808L11_exp200803_MS299_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G011_200808L11_exp200803_MS299_SCD_RAPA-40min_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 G011_200808L11_exp200803_MS299_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G011_200808L11_exp200803_MS299_SCD_RAPA-40min_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 G011_200808L11_exp200803_MS299_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G011_200808L11_exp200803_MS299_SCD_RAPA-40min_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 G011_200808L11_exp200803_MS299_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G011_200808L11_exp200803_MS299_SCD_RAPA-40min_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 G012_200808L12_exp200803_MS289_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G012_200808L12_exp200803_MS289_SCD_RAPA-65min_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 G012_200808L12_exp200803_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G012_200808L12_exp200803_MS289_SCD_RAPA-65min_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 G012_200808L12_exp200803_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G012_200808L12_exp200803_MS289_SCD_RAPA-65min_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 G012_200808L12_exp200803_MS289_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G012_200808L12_exp200803_MS289_SCD_RAPA-65min_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 G012_200808L12_exp200803_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G012_200808L12_exp200803_MS289_SCD_RAPA-65min_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 G012_200808L12_exp200803_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G012_200808L12_exp200803_MS289_SCD_RAPA-65min_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 G013_200808L13_exp200802_MS207_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G013_200808L13_exp200802_MS207_SCD_RAPA-40min_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 G013_200808L13_exp200802_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G013_200808L13_exp200802_MS207_SCD_RAPA-40min_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 G013_200808L13_exp200802_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G013_200808L13_exp200802_MS207_SCD_RAPA-40min_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 G013_200808L13_exp200802_MS207_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G013_200808L13_exp200802_MS207_SCD_RAPA-40min_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 G013_200808L13_exp200802_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G013_200808L13_exp200802_MS207_SCD_RAPA-40min_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 G013_200808L13_exp200802_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G013_200808L13_exp200802_MS207_SCD_RAPA-40min_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 G014_200808L14_exp200802_MS208_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G014_200808L14_exp200802_MS208_SCD_RAPA-40min_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 G014_200808L14_exp200802_MS208_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G014_200808L14_exp200802_MS208_SCD_RAPA-40min_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 G014_200808L14_exp200802_MS208_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G014_200808L14_exp200802_MS208_SCD_RAPA-40min_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 G014_200808L14_exp200802_MS208_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G014_200808L14_exp200802_MS208_SCD_RAPA-40min_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 G014_200808L14_exp200802_MS208_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G014_200808L14_exp200802_MS208_SCD_RAPA-40min_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 G014_200808L14_exp200802_MS208_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G014_200808L14_exp200802_MS208_SCD_RAPA-40min_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 G015_200808L15_exp200802_MS209_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G015_200808L15_exp200802_MS209_SCD_RAPA-40min_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 G015_200808L15_exp200802_MS209_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G015_200808L15_exp200802_MS209_SCD_RAPA-40min_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 G015_200808L15_exp200802_MS209_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G015_200808L15_exp200802_MS209_SCD_RAPA-40min_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 G015_200808L15_exp200802_MS209_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G015_200808L15_exp200802_MS209_SCD_RAPA-40min_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 G015_200808L15_exp200802_MS209_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G015_200808L15_exp200802_MS209_SCD_RAPA-40min_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 G015_200808L15_exp200802_MS209_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G015_200808L15_exp200802_MS209_SCD_RAPA-40min_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 G016_200808L16_exp200802_MS282_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G016_200808L16_exp200802_MS282_SCD_RAPA-40min_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 G016_200808L16_exp200802_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G016_200808L16_exp200802_MS282_SCD_RAPA-40min_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 G016_200808L16_exp200802_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G016_200808L16_exp200802_MS282_SCD_RAPA-40min_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 G016_200808L16_exp200802_MS282_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G016_200808L16_exp200802_MS282_SCD_RAPA-40min_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 G016_200808L16_exp200802_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G016_200808L16_exp200802_MS282_SCD_RAPA-40min_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 G016_200808L16_exp200802_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G016_200808L16_exp200802_MS282_SCD_RAPA-40min_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 G017_200808L17_exp200802_MS295_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G017_200808L17_exp200802_MS295_SCD_RAPA-40min_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 G017_200808L17_exp200802_MS295_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G017_200808L17_exp200802_MS295_SCD_RAPA-40min_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 G017_200808L17_exp200802_MS295_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G017_200808L17_exp200802_MS295_SCD_RAPA-40min_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 G017_200808L17_exp200802_MS295_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G017_200808L17_exp200802_MS295_SCD_RAPA-40min_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 G017_200808L17_exp200802_MS295_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G017_200808L17_exp200802_MS295_SCD_RAPA-40min_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 G017_200808L17_exp200802_MS295_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G017_200808L17_exp200802_MS295_SCD_RAPA-40min_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 G018_200808L18_exp200802_MS289_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G018_200808L18_exp200802_MS289_SCD_RAPA-65min_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 G018_200808L18_exp200802_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G018_200808L18_exp200802_MS289_SCD_RAPA-65min_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 G018_200808L18_exp200802_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G018_200808L18_exp200802_MS289_SCD_RAPA-65min_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 G018_200808L18_exp200802_MS289_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G018_200808L18_exp200802_MS289_SCD_RAPA-65min_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 G018_200808L18_exp200802_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G018_200808L18_exp200802_MS289_SCD_RAPA-65min_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 G018_200808L18_exp200802_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G018_200808L18_exp200802_MS289_SCD_RAPA-65min_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 G019_200808L19_exp200803_MS207_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G019_200808L19_exp200803_MS207_SCD_RAPA-40min_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 G019_200808L19_exp200803_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G019_200808L19_exp200803_MS207_SCD_RAPA-40min_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 G019_200808L19_exp200803_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G019_200808L19_exp200803_MS207_SCD_RAPA-40min_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 G019_200808L19_exp200803_MS207_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G019_200808L19_exp200803_MS207_SCD_RAPA-40min_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 G019_200808L19_exp200803_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G019_200808L19_exp200803_MS207_SCD_RAPA-40min_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 G019_200808L19_exp200803_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G019_200808L19_exp200803_MS207_SCD_RAPA-40min_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 G020_200808L20_exp200803_MS281_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G020_200808L20_exp200803_MS281_SCD_RAPA-40min_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 G020_200808L20_exp200803_MS281_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G020_200808L20_exp200803_MS281_SCD_RAPA-40min_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 G020_200808L20_exp200803_MS281_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G020_200808L20_exp200803_MS281_SCD_RAPA-40min_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 G020_200808L20_exp200803_MS281_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G020_200808L20_exp200803_MS281_SCD_RAPA-40min_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 G020_200808L20_exp200803_MS281_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G020_200808L20_exp200803_MS281_SCD_RAPA-40min_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 G020_200808L20_exp200803_MS281_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G020_200808L20_exp200803_MS281_SCD_RAPA-40min_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 G021_200808L21_exp200803_MS282_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G021_200808L21_exp200803_MS282_SCD_RAPA-40min_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 G021_200808L21_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G021_200808L21_exp200803_MS282_SCD_RAPA-40min_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 G021_200808L21_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G021_200808L21_exp200803_MS282_SCD_RAPA-40min_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 G021_200808L21_exp200803_MS282_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G021_200808L21_exp200803_MS282_SCD_RAPA-40min_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 G021_200808L21_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G021_200808L21_exp200803_MS282_SCD_RAPA-40min_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 G021_200808L21_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G021_200808L21_exp200803_MS282_SCD_RAPA-40min_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 G022_200808L22_exp200803_MS294_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G022_200808L22_exp200803_MS294_SCD_RAPA-40min_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 G022_200808L22_exp200803_MS294_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G022_200808L22_exp200803_MS294_SCD_RAPA-40min_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 G022_200808L22_exp200803_MS294_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G022_200808L22_exp200803_MS294_SCD_RAPA-40min_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 G022_200808L22_exp200803_MS294_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G022_200808L22_exp200803_MS294_SCD_RAPA-40min_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 G022_200808L22_exp200803_MS294_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G022_200808L22_exp200803_MS294_SCD_RAPA-40min_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 G022_200808L22_exp200803_MS294_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G022_200808L22_exp200803_MS294_SCD_RAPA-40min_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 G023_200808L23_exp200803_MS299_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G023_200808L23_exp200803_MS299_SCD_RAPA-40min_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 G023_200808L23_exp200803_MS299_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G023_200808L23_exp200803_MS299_SCD_RAPA-40min_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 G023_200808L23_exp200803_MS299_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G023_200808L23_exp200803_MS299_SCD_RAPA-40min_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 G023_200808L23_exp200803_MS299_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G023_200808L23_exp200803_MS299_SCD_RAPA-40min_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 G023_200808L23_exp200803_MS299_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G023_200808L23_exp200803_MS299_SCD_RAPA-40min_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 G023_200808L23_exp200803_MS299_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G023_200808L23_exp200803_MS299_SCD_RAPA-40min_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 G024_200808L24_exp200803_MS289_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G024_200808L24_exp200803_MS289_SCD_RAPA-65min_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 G024_200808L24_exp200803_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G024_200808L24_exp200803_MS289_SCD_RAPA-65min_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 G024_200808L24_exp200803_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G024_200808L24_exp200803_MS289_SCD_RAPA-65min_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 G024_200808L24_exp200803_MS289_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G024_200808L24_exp200803_MS289_SCD_RAPA-65min_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 G024_200808L24_exp200803_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G024_200808L24_exp200803_MS289_SCD_RAPA-65min_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 G024_200808L24_exp200803_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G024_200808L24_exp200803_MS289_SCD_RAPA-65min_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 G025_200917L29_exp200802_MS207_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G025_200917L29_exp200802_MS207_SCD_RAPA-40min_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 G025_200917L29_exp200802_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G025_200917L29_exp200802_MS207_SCD_RAPA-40min_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 G025_200917L29_exp200802_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G025_200917L29_exp200802_MS207_SCD_RAPA-40min_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 G025_200917L29_exp200802_MS207_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G025_200917L29_exp200802_MS207_SCD_RAPA-40min_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 G025_200917L29_exp200802_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G025_200917L29_exp200802_MS207_SCD_RAPA-40min_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 G025_200917L29_exp200802_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G025_200917L29_exp200802_MS207_SCD_RAPA-40min_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 G026_200917L30_exp200802_MS208_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G026_200917L30_exp200802_MS208_SCD_RAPA-40min_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 G026_200917L30_exp200802_MS208_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G026_200917L30_exp200802_MS208_SCD_RAPA-40min_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 G026_200917L30_exp200802_MS208_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G026_200917L30_exp200802_MS208_SCD_RAPA-40min_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 G026_200917L30_exp200802_MS208_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G026_200917L30_exp200802_MS208_SCD_RAPA-40min_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 G026_200917L30_exp200802_MS208_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G026_200917L30_exp200802_MS208_SCD_RAPA-40min_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 G026_200917L30_exp200802_MS208_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G026_200917L30_exp200802_MS208_SCD_RAPA-40min_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 G027_200917L31_exp200802_MS209_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G027_200917L31_exp200802_MS209_SCD_RAPA-40min_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 G027_200917L31_exp200802_MS209_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G027_200917L31_exp200802_MS209_SCD_RAPA-40min_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 G027_200917L31_exp200802_MS209_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G027_200917L31_exp200802_MS209_SCD_RAPA-40min_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 G027_200917L31_exp200802_MS209_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G027_200917L31_exp200802_MS209_SCD_RAPA-40min_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 G027_200917L31_exp200802_MS209_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G027_200917L31_exp200802_MS209_SCD_RAPA-40min_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 G027_200917L31_exp200802_MS209_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G027_200917L31_exp200802_MS209_SCD_RAPA-40min_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 G028_200917L37_exp200802_MS282_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G028_200917L37_exp200802_MS282_SCD_RAPA-40min_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 G028_200917L37_exp200802_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G028_200917L37_exp200802_MS282_SCD_RAPA-40min_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 G028_200917L37_exp200802_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G028_200917L37_exp200802_MS282_SCD_RAPA-40min_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 G028_200917L37_exp200802_MS282_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G028_200917L37_exp200802_MS282_SCD_RAPA-40min_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 G028_200917L37_exp200802_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G028_200917L37_exp200802_MS282_SCD_RAPA-40min_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 G028_200917L37_exp200802_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G028_200917L37_exp200802_MS282_SCD_RAPA-40min_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 G029_200917L33_exp200802_MS295_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G029_200917L33_exp200802_MS295_SCD_RAPA-40min_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 G029_200917L33_exp200802_MS295_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G029_200917L33_exp200802_MS295_SCD_RAPA-40min_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 G029_200917L33_exp200802_MS295_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G029_200917L33_exp200802_MS295_SCD_RAPA-40min_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 G029_200917L33_exp200802_MS295_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G029_200917L33_exp200802_MS295_SCD_RAPA-40min_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 G029_200917L33_exp200802_MS295_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G029_200917L33_exp200802_MS295_SCD_RAPA-40min_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 G029_200917L33_exp200802_MS295_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G029_200917L33_exp200802_MS295_SCD_RAPA-40min_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 G030_200917L34_exp200802_MS289_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G030_200917L34_exp200802_MS289_SCD_RAPA-65min_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 G030_200917L34_exp200802_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G030_200917L34_exp200802_MS289_SCD_RAPA-65min_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 G030_200917L34_exp200802_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G030_200917L34_exp200802_MS289_SCD_RAPA-65min_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 G030_200917L34_exp200802_MS289_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G030_200917L34_exp200802_MS289_SCD_RAPA-65min_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 G030_200917L34_exp200802_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G030_200917L34_exp200802_MS289_SCD_RAPA-65min_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 G030_200917L34_exp200802_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G030_200917L34_exp200802_MS289_SCD_RAPA-65min_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 G031_200917L35_exp200803_MS207_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G031_200917L35_exp200803_MS207_SCD_RAPA-40min_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 G031_200917L35_exp200803_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G031_200917L35_exp200803_MS207_SCD_RAPA-40min_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 G031_200917L35_exp200803_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G031_200917L35_exp200803_MS207_SCD_RAPA-40min_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 G031_200917L35_exp200803_MS207_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G031_200917L35_exp200803_MS207_SCD_RAPA-40min_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 G031_200917L35_exp200803_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G031_200917L35_exp200803_MS207_SCD_RAPA-40min_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 G031_200917L35_exp200803_MS207_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G031_200917L35_exp200803_MS207_SCD_RAPA-40min_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 G032_200917L36_exp200803_MS281_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G032_200917L36_exp200803_MS281_SCD_RAPA-40min_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 G032_200917L36_exp200803_MS281_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G032_200917L36_exp200803_MS281_SCD_RAPA-40min_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 G032_200917L36_exp200803_MS281_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G032_200917L36_exp200803_MS281_SCD_RAPA-40min_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 G032_200917L36_exp200803_MS281_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G032_200917L36_exp200803_MS281_SCD_RAPA-40min_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 G032_200917L36_exp200803_MS281_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G032_200917L36_exp200803_MS281_SCD_RAPA-40min_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 G032_200917L36_exp200803_MS281_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G032_200917L36_exp200803_MS281_SCD_RAPA-40min_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 G033_200917L32_exp200803_MS282_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G033_200917L32_exp200803_MS282_SCD_RAPA-40min_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 G033_200917L32_exp200803_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G033_200917L32_exp200803_MS282_SCD_RAPA-40min_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 G033_200917L32_exp200803_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G033_200917L32_exp200803_MS282_SCD_RAPA-40min_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 G033_200917L32_exp200803_MS282_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G033_200917L32_exp200803_MS282_SCD_RAPA-40min_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 G033_200917L32_exp200803_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G033_200917L32_exp200803_MS282_SCD_RAPA-40min_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 G033_200917L32_exp200803_MS282_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G033_200917L32_exp200803_MS282_SCD_RAPA-40min_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 G034_200917L38_exp200803_MS294_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G034_200917L38_exp200803_MS294_SCD_RAPA-40min_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 G034_200917L38_exp200803_MS294_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G034_200917L38_exp200803_MS294_SCD_RAPA-40min_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 G034_200917L38_exp200803_MS294_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G034_200917L38_exp200803_MS294_SCD_RAPA-40min_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 G034_200917L38_exp200803_MS294_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G034_200917L38_exp200803_MS294_SCD_RAPA-40min_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 G034_200917L38_exp200803_MS294_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G034_200917L38_exp200803_MS294_SCD_RAPA-40min_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 G034_200917L38_exp200803_MS294_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G034_200917L38_exp200803_MS294_SCD_RAPA-40min_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 G035_200917L39_exp200803_MS299_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G035_200917L39_exp200803_MS299_SCD_RAPA-40min_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 G035_200917L39_exp200803_MS299_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G035_200917L39_exp200803_MS299_SCD_RAPA-40min_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 G035_200917L39_exp200803_MS299_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G035_200917L39_exp200803_MS299_SCD_RAPA-40min_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 G035_200917L39_exp200803_MS299_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G035_200917L39_exp200803_MS299_SCD_RAPA-40min_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 G035_200917L39_exp200803_MS299_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G035_200917L39_exp200803_MS299_SCD_RAPA-40min_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 G035_200917L39_exp200803_MS299_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G035_200917L39_exp200803_MS299_SCD_RAPA-40min_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 G036_200917L40_exp200803_MS289_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G036_200917L40_exp200803_MS289_SCD_RAPA-65min_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 G036_200917L40_exp200803_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G036_200917L40_exp200803_MS289_SCD_RAPA-65min_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 G036_200917L40_exp200803_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G036_200917L40_exp200803_MS289_SCD_RAPA-65min_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 G036_200917L40_exp200803_MS289_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G036_200917L40_exp200803_MS289_SCD_RAPA-65min_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 G036_200917L40_exp200803_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G036_200917L40_exp200803_MS289_SCD_RAPA-65min_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 G036_200917L40_exp200803_MS289_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G036_200917L40_exp200803_MS289_SCD_RAPA-65min_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 G037_200917L01_exp200802_MS207_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G037_200917L01_exp200802_MS207_SCD_RAPA-40min_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 G037_200917L01_exp200802_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G037_200917L01_exp200802_MS207_SCD_RAPA-40min_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 G037_200917L01_exp200802_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G037_200917L01_exp200802_MS207_SCD_RAPA-40min_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 G037_200917L01_exp200802_MS207_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G037_200917L01_exp200802_MS207_SCD_RAPA-40min_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 G037_200917L01_exp200802_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G037_200917L01_exp200802_MS207_SCD_RAPA-40min_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 G037_200917L01_exp200802_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G037_200917L01_exp200802_MS207_SCD_RAPA-40min_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 G038_200917L02_exp200802_MS208_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G038_200917L02_exp200802_MS208_SCD_RAPA-40min_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 G038_200917L02_exp200802_MS208_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G038_200917L02_exp200802_MS208_SCD_RAPA-40min_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 G038_200917L02_exp200802_MS208_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G038_200917L02_exp200802_MS208_SCD_RAPA-40min_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 G038_200917L02_exp200802_MS208_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G038_200917L02_exp200802_MS208_SCD_RAPA-40min_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 G038_200917L02_exp200802_MS208_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G038_200917L02_exp200802_MS208_SCD_RAPA-40min_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 G038_200917L02_exp200802_MS208_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G038_200917L02_exp200802_MS208_SCD_RAPA-40min_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 G039_200917L03_exp200802_MS209_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G039_200917L03_exp200802_MS209_SCD_RAPA-40min_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 G039_200917L03_exp200802_MS209_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G039_200917L03_exp200802_MS209_SCD_RAPA-40min_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 G039_200917L03_exp200802_MS209_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G039_200917L03_exp200802_MS209_SCD_RAPA-40min_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 G039_200917L03_exp200802_MS209_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G039_200917L03_exp200802_MS209_SCD_RAPA-40min_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 G039_200917L03_exp200802_MS209_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G039_200917L03_exp200802_MS209_SCD_RAPA-40min_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 G039_200917L03_exp200802_MS209_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G039_200917L03_exp200802_MS209_SCD_RAPA-40min_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 G040_200917L05_exp200802_MS295_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G040_200917L05_exp200802_MS295_SCD_RAPA-40min_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 G040_200917L05_exp200802_MS295_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G040_200917L05_exp200802_MS295_SCD_RAPA-40min_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 G040_200917L05_exp200802_MS295_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G040_200917L05_exp200802_MS295_SCD_RAPA-40min_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 G040_200917L05_exp200802_MS295_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G040_200917L05_exp200802_MS295_SCD_RAPA-40min_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 G040_200917L05_exp200802_MS295_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G040_200917L05_exp200802_MS295_SCD_RAPA-40min_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 G040_200917L05_exp200802_MS295_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G040_200917L05_exp200802_MS295_SCD_RAPA-40min_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 G041_200917L06_exp200802_MS289_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G041_200917L06_exp200802_MS289_SCD_RAPA-65min_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 G041_200917L06_exp200802_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G041_200917L06_exp200802_MS289_SCD_RAPA-65min_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 G041_200917L06_exp200802_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G041_200917L06_exp200802_MS289_SCD_RAPA-65min_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 G041_200917L06_exp200802_MS289_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G041_200917L06_exp200802_MS289_SCD_RAPA-65min_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 G041_200917L06_exp200802_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G041_200917L06_exp200802_MS289_SCD_RAPA-65min_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 G041_200917L06_exp200802_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G041_200917L06_exp200802_MS289_SCD_RAPA-65min_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 G042_200917L07_exp200803_MS207_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G042_200917L07_exp200803_MS207_SCD_RAPA-40min_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 G042_200917L07_exp200803_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G042_200917L07_exp200803_MS207_SCD_RAPA-40min_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 G042_200917L07_exp200803_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G042_200917L07_exp200803_MS207_SCD_RAPA-40min_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 G042_200917L07_exp200803_MS207_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G042_200917L07_exp200803_MS207_SCD_RAPA-40min_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 G042_200917L07_exp200803_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G042_200917L07_exp200803_MS207_SCD_RAPA-40min_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 G042_200917L07_exp200803_MS207_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G042_200917L07_exp200803_MS207_SCD_RAPA-40min_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 G043_200917L08_exp200803_MS281_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G043_200917L08_exp200803_MS281_SCD_RAPA-40min_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 G043_200917L08_exp200803_MS281_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G043_200917L08_exp200803_MS281_SCD_RAPA-40min_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 G043_200917L08_exp200803_MS281_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G043_200917L08_exp200803_MS281_SCD_RAPA-40min_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 G043_200917L08_exp200803_MS281_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G043_200917L08_exp200803_MS281_SCD_RAPA-40min_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 G043_200917L08_exp200803_MS281_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G043_200917L08_exp200803_MS281_SCD_RAPA-40min_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 G043_200917L08_exp200803_MS281_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G043_200917L08_exp200803_MS281_SCD_RAPA-40min_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 G044_200917L09_exp200803_MS282_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G044_200917L09_exp200803_MS282_SCD_RAPA-40min_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 G044_200917L09_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G044_200917L09_exp200803_MS282_SCD_RAPA-40min_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 G044_200917L09_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G044_200917L09_exp200803_MS282_SCD_RAPA-40min_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 G044_200917L09_exp200803_MS282_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G044_200917L09_exp200803_MS282_SCD_RAPA-40min_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 G044_200917L09_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G044_200917L09_exp200803_MS282_SCD_RAPA-40min_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 G044_200917L09_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G044_200917L09_exp200803_MS282_SCD_RAPA-40min_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 G045_200917L10_exp200803_MS294_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G045_200917L10_exp200803_MS294_SCD_RAPA-40min_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 G045_200917L10_exp200803_MS294_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G045_200917L10_exp200803_MS294_SCD_RAPA-40min_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 G045_200917L10_exp200803_MS294_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G045_200917L10_exp200803_MS294_SCD_RAPA-40min_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 G045_200917L10_exp200803_MS294_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G045_200917L10_exp200803_MS294_SCD_RAPA-40min_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 G045_200917L10_exp200803_MS294_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G045_200917L10_exp200803_MS294_SCD_RAPA-40min_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 G045_200917L10_exp200803_MS294_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G045_200917L10_exp200803_MS294_SCD_RAPA-40min_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 G046_200917L11_exp200803_MS299_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G046_200917L11_exp200803_MS299_SCD_RAPA-40min_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 G046_200917L11_exp200803_MS299_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G046_200917L11_exp200803_MS299_SCD_RAPA-40min_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 G046_200917L11_exp200803_MS299_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G046_200917L11_exp200803_MS299_SCD_RAPA-40min_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 G046_200917L11_exp200803_MS299_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G046_200917L11_exp200803_MS299_SCD_RAPA-40min_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 G046_200917L11_exp200803_MS299_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G046_200917L11_exp200803_MS299_SCD_RAPA-40min_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 G046_200917L11_exp200803_MS299_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G046_200917L11_exp200803_MS299_SCD_RAPA-40min_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 G047_200917L12_exp200803_MS289_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G047_200917L12_exp200803_MS289_SCD_RAPA-65min_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 G047_200917L12_exp200803_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G047_200917L12_exp200803_MS289_SCD_RAPA-65min_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 G047_200917L12_exp200803_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G047_200917L12_exp200803_MS289_SCD_RAPA-65min_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 G047_200917L12_exp200803_MS289_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G047_200917L12_exp200803_MS289_SCD_RAPA-65min_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 G047_200917L12_exp200803_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G047_200917L12_exp200803_MS289_SCD_RAPA-65min_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 G047_200917L12_exp200803_MS289_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G047_200917L12_exp200803_MS289_SCD_RAPA-65min_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 G048_200917L04_exp200803_MS282_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G048_200917L04_exp200803_MS282_SCD_RAPA-40min_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 G048_200917L04_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G048_200917L04_exp200803_MS282_SCD_RAPA-40min_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 G048_200917L04_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G048_200917L04_exp200803_MS282_SCD_RAPA-40min_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 G048_200917L04_exp200803_MS282_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G048_200917L04_exp200803_MS282_SCD_RAPA-40min_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 G048_200917L04_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G048_200917L04_exp200803_MS282_SCD_RAPA-40min_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 G048_200917L04_exp200803_MS282_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G048_200917L04_exp200803_MS282_SCD_RAPA-40min_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 G049_210325L13_exp2102_MS207_SCD_DMSO-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G049_210325L13_exp2102_MS207_SCD_DMSO-40min_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 G049_210325L13_exp2102_MS207_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G049_210325L13_exp2102_MS207_SCD_DMSO-40min_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 G049_210325L13_exp2102_MS207_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G049_210325L13_exp2102_MS207_SCD_DMSO-40min_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 G049_210325L13_exp2102_MS207_SCD_DMSO-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G049_210325L13_exp2102_MS207_SCD_DMSO-40min_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 G049_210325L13_exp2102_MS207_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G049_210325L13_exp2102_MS207_SCD_DMSO-40min_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 G049_210325L13_exp2102_MS207_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G049_210325L13_exp2102_MS207_SCD_DMSO-40min_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 G050_210325L14_exp2102_MS289_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G050_210325L14_exp2102_MS289_SCD_RAPA-60min_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 G050_210325L14_exp2102_MS289_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G050_210325L14_exp2102_MS289_SCD_RAPA-60min_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 G050_210325L14_exp2102_MS289_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G050_210325L14_exp2102_MS289_SCD_RAPA-60min_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 G050_210325L14_exp2102_MS289_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G050_210325L14_exp2102_MS289_SCD_RAPA-60min_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 G050_210325L14_exp2102_MS289_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G050_210325L14_exp2102_MS289_SCD_RAPA-60min_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 G050_210325L14_exp2102_MS289_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G050_210325L14_exp2102_MS289_SCD_RAPA-60min_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 G051_210325L15_exp2102_MS305_SCD_DMSO-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G051_210325L15_exp2102_MS305_SCD_DMSO-40min_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 G051_210325L15_exp2102_MS305_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G051_210325L15_exp2102_MS305_SCD_DMSO-40min_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 G051_210325L15_exp2102_MS305_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G051_210325L15_exp2102_MS305_SCD_DMSO-40min_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 G051_210325L15_exp2102_MS305_SCD_DMSO-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G051_210325L15_exp2102_MS305_SCD_DMSO-40min_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 G051_210325L15_exp2102_MS305_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G051_210325L15_exp2102_MS305_SCD_DMSO-40min_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 G051_210325L15_exp2102_MS305_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G051_210325L15_exp2102_MS305_SCD_DMSO-40min_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 G052_210325L16_exp2102_MS305_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G052_210325L16_exp2102_MS305_SCD_RAPA-40min_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 G052_210325L16_exp2102_MS305_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G052_210325L16_exp2102_MS305_SCD_RAPA-40min_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 G052_210325L16_exp2102_MS305_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G052_210325L16_exp2102_MS305_SCD_RAPA-40min_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 G052_210325L16_exp2102_MS305_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G052_210325L16_exp2102_MS305_SCD_RAPA-40min_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 G052_210325L16_exp2102_MS305_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G052_210325L16_exp2102_MS305_SCD_RAPA-40min_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 G052_210325L16_exp2102_MS305_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G052_210325L16_exp2102_MS305_SCD_RAPA-40min_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 G053_210325L17_exp2102_MS306_SCD_DMSO-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G053_210325L17_exp2102_MS306_SCD_DMSO-40min_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 G053_210325L17_exp2102_MS306_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G053_210325L17_exp2102_MS306_SCD_DMSO-40min_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 G053_210325L17_exp2102_MS306_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G053_210325L17_exp2102_MS306_SCD_DMSO-40min_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 G053_210325L17_exp2102_MS306_SCD_DMSO-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G053_210325L17_exp2102_MS306_SCD_DMSO-40min_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 G053_210325L17_exp2102_MS306_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G053_210325L17_exp2102_MS306_SCD_DMSO-40min_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 G053_210325L17_exp2102_MS306_SCD_DMSO-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G053_210325L17_exp2102_MS306_SCD_DMSO-40min_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 G054_210325L18_exp2102_MS306_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G054_210325L18_exp2102_MS306_SCD_RAPA-40min_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 G054_210325L18_exp2102_MS306_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G054_210325L18_exp2102_MS306_SCD_RAPA-40min_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 G054_210325L18_exp2102_MS306_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G054_210325L18_exp2102_MS306_SCD_RAPA-40min_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 G054_210325L18_exp2102_MS306_SCD_RAPA-40min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G054_210325L18_exp2102_MS306_SCD_RAPA-40min_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 G054_210325L18_exp2102_MS306_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G054_210325L18_exp2102_MS306_SCD_RAPA-40min_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 G054_210325L18_exp2102_MS306_SCD_RAPA-40min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G054_210325L18_exp2102_MS306_SCD_RAPA-40min_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 G055_210325L31_exp2102_MS207_SCD_DMSO-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G055_210325L31_exp2102_MS207_SCD_DMSO-40min_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 G055_210325L31_exp2102_MS207_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G055_210325L31_exp2102_MS207_SCD_DMSO-40min_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 G055_210325L31_exp2102_MS207_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G055_210325L31_exp2102_MS207_SCD_DMSO-40min_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 G055_210325L31_exp2102_MS207_SCD_DMSO-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G055_210325L31_exp2102_MS207_SCD_DMSO-40min_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 G055_210325L31_exp2102_MS207_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G055_210325L31_exp2102_MS207_SCD_DMSO-40min_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 G055_210325L31_exp2102_MS207_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G055_210325L31_exp2102_MS207_SCD_DMSO-40min_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 G056_210325L32_exp2102_MS289_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G056_210325L32_exp2102_MS289_SCD_RAPA-60min_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 G056_210325L32_exp2102_MS289_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G056_210325L32_exp2102_MS289_SCD_RAPA-60min_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 G056_210325L32_exp2102_MS289_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G056_210325L32_exp2102_MS289_SCD_RAPA-60min_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 G056_210325L32_exp2102_MS289_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G056_210325L32_exp2102_MS289_SCD_RAPA-60min_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 G056_210325L32_exp2102_MS289_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G056_210325L32_exp2102_MS289_SCD_RAPA-60min_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 G056_210325L32_exp2102_MS289_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G056_210325L32_exp2102_MS289_SCD_RAPA-60min_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 G057_210325L33_exp2102_MS305_SCD_DMSO-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G057_210325L33_exp2102_MS305_SCD_DMSO-40min_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 G057_210325L33_exp2102_MS305_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G057_210325L33_exp2102_MS305_SCD_DMSO-40min_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 G057_210325L33_exp2102_MS305_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G057_210325L33_exp2102_MS305_SCD_DMSO-40min_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 G057_210325L33_exp2102_MS305_SCD_DMSO-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G057_210325L33_exp2102_MS305_SCD_DMSO-40min_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 G057_210325L33_exp2102_MS305_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G057_210325L33_exp2102_MS305_SCD_DMSO-40min_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 G057_210325L33_exp2102_MS305_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G057_210325L33_exp2102_MS305_SCD_DMSO-40min_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 G058_210325L34_exp2102_MS305_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G058_210325L34_exp2102_MS305_SCD_RAPA-40min_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 G058_210325L34_exp2102_MS305_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G058_210325L34_exp2102_MS305_SCD_RAPA-40min_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 G058_210325L34_exp2102_MS305_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G058_210325L34_exp2102_MS305_SCD_RAPA-40min_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 G058_210325L34_exp2102_MS305_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G058_210325L34_exp2102_MS305_SCD_RAPA-40min_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 G058_210325L34_exp2102_MS305_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G058_210325L34_exp2102_MS305_SCD_RAPA-40min_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 G058_210325L34_exp2102_MS305_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G058_210325L34_exp2102_MS305_SCD_RAPA-40min_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 G059_210325L35_exp2102_MS306_SCD_DMSO-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G059_210325L35_exp2102_MS306_SCD_DMSO-40min_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 G059_210325L35_exp2102_MS306_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G059_210325L35_exp2102_MS306_SCD_DMSO-40min_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 G059_210325L35_exp2102_MS306_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G059_210325L35_exp2102_MS306_SCD_DMSO-40min_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 G059_210325L35_exp2102_MS306_SCD_DMSO-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G059_210325L35_exp2102_MS306_SCD_DMSO-40min_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 G059_210325L35_exp2102_MS306_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G059_210325L35_exp2102_MS306_SCD_DMSO-40min_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 G059_210325L35_exp2102_MS306_SCD_DMSO-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G059_210325L35_exp2102_MS306_SCD_DMSO-40min_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 G060_210325L36_exp2102_MS306_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G060_210325L36_exp2102_MS306_SCD_RAPA-40min_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 G060_210325L36_exp2102_MS306_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G060_210325L36_exp2102_MS306_SCD_RAPA-40min_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 G060_210325L36_exp2102_MS306_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G060_210325L36_exp2102_MS306_SCD_RAPA-40min_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 G060_210325L36_exp2102_MS306_SCD_RAPA-40min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-G060_210325L36_exp2102_MS306_SCD_RAPA-40min_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 G060_210325L36_exp2102_MS306_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G060_210325L36_exp2102_MS306_SCD_RAPA-40min_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 G060_210325L36_exp2102_MS306_SCD_RAPA-40min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-G060_210325L36_exp2102_MS306_SCD_RAPA-40min_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 H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.1x36mers.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 H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.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 H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.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 H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H001_200201L43_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.1x36mers.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 H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.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 H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.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 H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H002_200201L44_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.1x36mers.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 H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.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 H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.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 H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H003_200201L45_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.1x36mers.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 H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.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 H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.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 H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H004_200201L46_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.1x36mers.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 H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.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 H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.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 H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H005_200201L47_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.1x36mers.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 H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.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 H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.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 H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H006_200201L48_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H007_200224L81_exp200118_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H007_200224L81_exp200118_MS207_SCD_RAPA-100min_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 H007_200224L81_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H007_200224L81_exp200118_MS207_SCD_RAPA-100min_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 H007_200224L81_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H007_200224L81_exp200118_MS207_SCD_RAPA-100min_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 H007_200224L81_exp200118_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H007_200224L81_exp200118_MS207_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H007_200224L81_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H007_200224L81_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H007_200224L81_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H007_200224L81_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H008_200224L82_exp200118_MS249_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H008_200224L82_exp200118_MS249_SCD_RAPA-100min_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 H008_200224L82_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H008_200224L82_exp200118_MS249_SCD_RAPA-100min_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 H008_200224L82_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H008_200224L82_exp200118_MS249_SCD_RAPA-100min_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 H008_200224L82_exp200118_MS249_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H008_200224L82_exp200118_MS249_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H008_200224L82_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H008_200224L82_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H008_200224L82_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H008_200224L82_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H009_200224L83_exp200118_MS250_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H009_200224L83_exp200118_MS250_SCD_RAPA-100min_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 H009_200224L83_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H009_200224L83_exp200118_MS250_SCD_RAPA-100min_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 H009_200224L83_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H009_200224L83_exp200118_MS250_SCD_RAPA-100min_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 H009_200224L83_exp200118_MS250_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H009_200224L83_exp200118_MS250_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H009_200224L83_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H009_200224L83_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H009_200224L83_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H009_200224L83_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H010_200224L84_exp200118_MS297_SCD_RAPA-040min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H010_200224L84_exp200118_MS297_SCD_RAPA-040min_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 H010_200224L84_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H010_200224L84_exp200118_MS297_SCD_RAPA-040min_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 H010_200224L84_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H010_200224L84_exp200118_MS297_SCD_RAPA-040min_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 H010_200224L84_exp200118_MS297_SCD_RAPA-040min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H010_200224L84_exp200118_MS297_SCD_RAPA-040min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H010_200224L84_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H010_200224L84_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H010_200224L84_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H010_200224L84_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H011_200224L85_exp200118_MS297_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H011_200224L85_exp200118_MS297_SCD_RAPA-100min_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 H011_200224L85_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H011_200224L85_exp200118_MS297_SCD_RAPA-100min_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 H011_200224L85_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H011_200224L85_exp200118_MS297_SCD_RAPA-100min_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 H011_200224L85_exp200118_MS297_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H011_200224L85_exp200118_MS297_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H011_200224L85_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H011_200224L85_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H011_200224L85_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H011_200224L85_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H012_200224L86_exp200118_MS297_SCD_RAPA-ON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H012_200224L86_exp200118_MS297_SCD_RAPA-ON_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 H012_200224L86_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H012_200224L86_exp200118_MS297_SCD_RAPA-ON_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 H012_200224L86_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H012_200224L86_exp200118_MS297_SCD_RAPA-ON_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 H012_200224L86_exp200118_MS297_SCD_RAPA-ON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H012_200224L86_exp200118_MS297_SCD_RAPA-ON_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H012_200224L86_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H012_200224L86_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H012_200224L86_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H012_200224L86_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.1x36mers.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 H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.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 H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.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 H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H013_200526L49_exp200118_MS207_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.1x36mers.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 H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.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 H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.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 H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H014_200526L50_exp200118_MS249_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.1x36mers.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 H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.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 H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.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 H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H015_200526L51_exp200118_MS250_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.1x36mers.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 H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.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 H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.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 H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H016_200526L52_exp200118_MS297_SCD_RAPA-040min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.1x36mers.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 H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.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 H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.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 H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H017_200526L53_exp200118_MS297_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.1x36mers.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 H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.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 H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.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 H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H018_200526L54_exp200118_MS297_SCD_RAPA-ON_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H019_200526L25_exp200118_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H019_200526L25_exp200118_MS207_SCD_RAPA-100min_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 H019_200526L25_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H019_200526L25_exp200118_MS207_SCD_RAPA-100min_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 H019_200526L25_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H019_200526L25_exp200118_MS207_SCD_RAPA-100min_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 H019_200526L25_exp200118_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H019_200526L25_exp200118_MS207_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H019_200526L25_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H019_200526L25_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H019_200526L25_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H019_200526L25_exp200118_MS207_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H020_200526L26_exp200118_MS249_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H020_200526L26_exp200118_MS249_SCD_RAPA-100min_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 H020_200526L26_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H020_200526L26_exp200118_MS249_SCD_RAPA-100min_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 H020_200526L26_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H020_200526L26_exp200118_MS249_SCD_RAPA-100min_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 H020_200526L26_exp200118_MS249_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H020_200526L26_exp200118_MS249_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H020_200526L26_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H020_200526L26_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H020_200526L26_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H020_200526L26_exp200118_MS249_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H021_200526L27_exp200118_MS250_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H021_200526L27_exp200118_MS250_SCD_RAPA-100min_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 H021_200526L27_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H021_200526L27_exp200118_MS250_SCD_RAPA-100min_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 H021_200526L27_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H021_200526L27_exp200118_MS250_SCD_RAPA-100min_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 H021_200526L27_exp200118_MS250_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H021_200526L27_exp200118_MS250_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H021_200526L27_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H021_200526L27_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H021_200526L27_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H021_200526L27_exp200118_MS250_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H022_200526L28_exp200118_MS297_SCD_RAPA-040min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H022_200526L28_exp200118_MS297_SCD_RAPA-040min_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 H022_200526L28_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H022_200526L28_exp200118_MS297_SCD_RAPA-040min_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 H022_200526L28_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H022_200526L28_exp200118_MS297_SCD_RAPA-040min_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 H022_200526L28_exp200118_MS297_SCD_RAPA-040min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H022_200526L28_exp200118_MS297_SCD_RAPA-040min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H022_200526L28_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H022_200526L28_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H022_200526L28_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H022_200526L28_exp200118_MS297_SCD_RAPA-040min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H023_200526L29_exp200118_MS297_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H023_200526L29_exp200118_MS297_SCD_RAPA-100min_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 H023_200526L29_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H023_200526L29_exp200118_MS297_SCD_RAPA-100min_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 H023_200526L29_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H023_200526L29_exp200118_MS297_SCD_RAPA-100min_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 H023_200526L29_exp200118_MS297_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H023_200526L29_exp200118_MS297_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H023_200526L29_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H023_200526L29_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H023_200526L29_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H023_200526L29_exp200118_MS297_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H024_200526L30_exp200118_MS297_SCD_RAPA-ON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H024_200526L30_exp200118_MS297_SCD_RAPA-ON_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 H024_200526L30_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H024_200526L30_exp200118_MS297_SCD_RAPA-ON_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 H024_200526L30_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H024_200526L30_exp200118_MS297_SCD_RAPA-ON_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 H024_200526L30_exp200118_MS297_SCD_RAPA-ON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H024_200526L30_exp200118_MS297_SCD_RAPA-ON_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H024_200526L30_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H024_200526L30_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H024_200526L30_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H024_200526L30_exp200118_MS297_SCD_RAPA-ON_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.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 H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.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 H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.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 H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H025_200917L17_exp200118_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.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 H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.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 H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.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 H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H026_200917L18_exp200118_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.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 H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.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 H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.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 H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H027_200917L19_exp200118_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.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 H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.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 H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.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 H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H028_200917L20_exp200118_MS297_SCD-RAPA-040min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.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 H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.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 H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.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 H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H029_200917L21_exp200118_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.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 H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.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 H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.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 H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H030_200917L22_exp200118_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.1x36mers.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 H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.2x36mers.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 H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.2x36mers.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 H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H031_200216L43_exp200205_MS207_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.1x36mers.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 H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.2x36mers.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 H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.2x36mers.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 H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H032_200216L44_exp200205_MS249_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.1x36mers.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 H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.2x36mers.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 H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.2x36mers.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 H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H033_200216L45_exp200205_MS250_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.1x36mers.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 H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.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 H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.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 H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H034_200216L46_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.1x36mers.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 H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.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 H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.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 H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H035_200216L47_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.1x36mers.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 H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.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 H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.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 H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H036_200216L48_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H037_200216L19_exp200205_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H037_200216L19_exp200205_MS207_SCD_RAPA-100min_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 H037_200216L19_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H037_200216L19_exp200205_MS207_SCD_RAPA-100min_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 H037_200216L19_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H037_200216L19_exp200205_MS207_SCD_RAPA-100min_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 H037_200216L19_exp200205_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H037_200216L19_exp200205_MS207_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H037_200216L19_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H037_200216L19_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H037_200216L19_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H037_200216L19_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H038_200216L20_exp200205_MS249_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H038_200216L20_exp200205_MS249_SCD_RAPA-100min_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 H038_200216L20_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H038_200216L20_exp200205_MS249_SCD_RAPA-100min_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 H038_200216L20_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H038_200216L20_exp200205_MS249_SCD_RAPA-100min_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 H038_200216L20_exp200205_MS249_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H038_200216L20_exp200205_MS249_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H038_200216L20_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H038_200216L20_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H038_200216L20_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H038_200216L20_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H039_200216L21_exp200205_MS250_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H039_200216L21_exp200205_MS250_SCD_RAPA-100min_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 H039_200216L21_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H039_200216L21_exp200205_MS250_SCD_RAPA-100min_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 H039_200216L21_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H039_200216L21_exp200205_MS250_SCD_RAPA-100min_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 H039_200216L21_exp200205_MS250_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H039_200216L21_exp200205_MS250_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H039_200216L21_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H039_200216L21_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H039_200216L21_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H039_200216L21_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H040_200216L22_exp200205_MS297_SCD_RAPA-040min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H040_200216L22_exp200205_MS297_SCD_RAPA-040min_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 H040_200216L22_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H040_200216L22_exp200205_MS297_SCD_RAPA-040min_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 H040_200216L22_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H040_200216L22_exp200205_MS297_SCD_RAPA-040min_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 H040_200216L22_exp200205_MS297_SCD_RAPA-040min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H040_200216L22_exp200205_MS297_SCD_RAPA-040min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H040_200216L22_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H040_200216L22_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H040_200216L22_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H040_200216L22_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H041_200216L23_exp200205_MS297_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H041_200216L23_exp200205_MS297_SCD_RAPA-100min_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 H041_200216L23_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H041_200216L23_exp200205_MS297_SCD_RAPA-100min_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 H041_200216L23_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H041_200216L23_exp200205_MS297_SCD_RAPA-100min_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 H041_200216L23_exp200205_MS297_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H041_200216L23_exp200205_MS297_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H041_200216L23_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H041_200216L23_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H041_200216L23_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H041_200216L23_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H042_200216L24_exp200205_MS297_SCD_RAPA-ON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H042_200216L24_exp200205_MS297_SCD_RAPA-ON_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 H042_200216L24_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H042_200216L24_exp200205_MS297_SCD_RAPA-ON_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 H042_200216L24_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H042_200216L24_exp200205_MS297_SCD_RAPA-ON_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 H042_200216L24_exp200205_MS297_SCD_RAPA-ON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H042_200216L24_exp200205_MS297_SCD_RAPA-ON_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H042_200216L24_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H042_200216L24_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H042_200216L24_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H042_200216L24_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.1x36mers.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 H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.2x36mers.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 H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.2x36mers.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 H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H043_200526L61_exp200205_MS207_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.1x36mers.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 H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.2x36mers.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 H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.2x36mers.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 H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H044_200526L62_exp200205_MS249_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.1x36mers.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 H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.2x36mers.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 H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.2x36mers.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 H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H045_200526L63_exp200205_MS250_SCD_RAPA_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.1x36mers.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 H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.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 H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.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 H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H046_200526L64_exp200205_MS297_SCD_RAPA-040min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.1x36mers.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 H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.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 H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.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 H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H047_200526L65_exp200205_MS297_SCD_RAPA-100min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.1x36mers.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 H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.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 H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.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 H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H048_200526L66_exp200205_MS297_SCD_RAPA-ON_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H049_200526L37_exp200205_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H049_200526L37_exp200205_MS207_SCD_RAPA-100min_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 H049_200526L37_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H049_200526L37_exp200205_MS207_SCD_RAPA-100min_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 H049_200526L37_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H049_200526L37_exp200205_MS207_SCD_RAPA-100min_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 H049_200526L37_exp200205_MS207_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H049_200526L37_exp200205_MS207_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H049_200526L37_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H049_200526L37_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H049_200526L37_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H049_200526L37_exp200205_MS207_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H050_200526L38_exp200205_MS249_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H050_200526L38_exp200205_MS249_SCD_RAPA-100min_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 H050_200526L38_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H050_200526L38_exp200205_MS249_SCD_RAPA-100min_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 H050_200526L38_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H050_200526L38_exp200205_MS249_SCD_RAPA-100min_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 H050_200526L38_exp200205_MS249_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H050_200526L38_exp200205_MS249_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H050_200526L38_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H050_200526L38_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H050_200526L38_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H050_200526L38_exp200205_MS249_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H051_200526L39_exp200205_MS250_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H051_200526L39_exp200205_MS250_SCD_RAPA-100min_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 H051_200526L39_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H051_200526L39_exp200205_MS250_SCD_RAPA-100min_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 H051_200526L39_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H051_200526L39_exp200205_MS250_SCD_RAPA-100min_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 H051_200526L39_exp200205_MS250_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H051_200526L39_exp200205_MS250_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H051_200526L39_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H051_200526L39_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H051_200526L39_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H051_200526L39_exp200205_MS250_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H052_200526L40_exp200205_MS297_SCD_RAPA-040min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H052_200526L40_exp200205_MS297_SCD_RAPA-040min_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 H052_200526L40_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H052_200526L40_exp200205_MS297_SCD_RAPA-040min_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 H052_200526L40_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H052_200526L40_exp200205_MS297_SCD_RAPA-040min_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 H052_200526L40_exp200205_MS297_SCD_RAPA-040min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H052_200526L40_exp200205_MS297_SCD_RAPA-040min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H052_200526L40_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H052_200526L40_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H052_200526L40_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H052_200526L40_exp200205_MS297_SCD_RAPA-040min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H053_200526L41_exp200205_MS297_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H053_200526L41_exp200205_MS297_SCD_RAPA-100min_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 H053_200526L41_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H053_200526L41_exp200205_MS297_SCD_RAPA-100min_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 H053_200526L41_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H053_200526L41_exp200205_MS297_SCD_RAPA-100min_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 H053_200526L41_exp200205_MS297_SCD_RAPA-100min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H053_200526L41_exp200205_MS297_SCD_RAPA-100min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H053_200526L41_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H053_200526L41_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H053_200526L41_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H053_200526L41_exp200205_MS297_SCD_RAPA-100min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H054_200526L42_exp200205_MS297_SCD_RAPA-ON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H054_200526L42_exp200205_MS297_SCD_RAPA-ON_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 H054_200526L42_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H054_200526L42_exp200205_MS297_SCD_RAPA-ON_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 H054_200526L42_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H054_200526L42_exp200205_MS297_SCD_RAPA-ON_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 H054_200526L42_exp200205_MS297_SCD_RAPA-ON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H054_200526L42_exp200205_MS297_SCD_RAPA-ON_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H054_200526L42_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H054_200526L42_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H054_200526L42_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H054_200526L42_exp200205_MS297_SCD_RAPA-ON_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.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 H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.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 H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.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 H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H055_200917L23_exp200205_MS207_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.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 H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.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 H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.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 H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H056_200917L24_exp200205_MS249_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.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 H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.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 H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.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 H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H057_200917L25_exp200205_MS250_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.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 H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.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 H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.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 H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H058_200917L26_exp200205_MS297_SCD-RAPA-40min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.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 H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.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 H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.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 H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H059_200917L27_exp200205_MS297_SCD-RAPA-100min_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.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 H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.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 H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.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 H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H060_200917L28_exp200205_MS297_SCD-RAPA-ON_AB107_rep.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H061_190807L19_exp190803_MS207_SCD_RAPA-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H061_190807L19_exp190803_MS207_SCD_RAPA-120min_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 H061_190807L19_exp190803_MS207_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H061_190807L19_exp190803_MS207_SCD_RAPA-120min_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 H061_190807L19_exp190803_MS207_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H061_190807L19_exp190803_MS207_SCD_RAPA-120min_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 H061_190807L19_exp190803_MS207_SCD_RAPA-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H061_190807L19_exp190803_MS207_SCD_RAPA-120min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H061_190807L19_exp190803_MS207_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H061_190807L19_exp190803_MS207_SCD_RAPA-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H061_190807L19_exp190803_MS207_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H061_190807L19_exp190803_MS207_SCD_RAPA-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H062_190807L20_exp190803_MS249_SCD_RAPA-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H062_190807L20_exp190803_MS249_SCD_RAPA-120min_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 H062_190807L20_exp190803_MS249_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H062_190807L20_exp190803_MS249_SCD_RAPA-120min_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 H062_190807L20_exp190803_MS249_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H062_190807L20_exp190803_MS249_SCD_RAPA-120min_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 H062_190807L20_exp190803_MS249_SCD_RAPA-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H062_190807L20_exp190803_MS249_SCD_RAPA-120min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H062_190807L20_exp190803_MS249_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H062_190807L20_exp190803_MS249_SCD_RAPA-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H062_190807L20_exp190803_MS249_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H062_190807L20_exp190803_MS249_SCD_RAPA-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H063_190807L21_exp190803_MS250_SCD_RAPA-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H063_190807L21_exp190803_MS250_SCD_RAPA-120min_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 H063_190807L21_exp190803_MS250_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H063_190807L21_exp190803_MS250_SCD_RAPA-120min_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 H063_190807L21_exp190803_MS250_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H063_190807L21_exp190803_MS250_SCD_RAPA-120min_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 H063_190807L21_exp190803_MS250_SCD_RAPA-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H063_190807L21_exp190803_MS250_SCD_RAPA-120min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H063_190807L21_exp190803_MS250_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H063_190807L21_exp190803_MS250_SCD_RAPA-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H063_190807L21_exp190803_MS250_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H063_190807L21_exp190803_MS250_SCD_RAPA-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H064_190807L22_exp190803_MS297_SCD_RAPA-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H064_190807L22_exp190803_MS297_SCD_RAPA-120min_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 H064_190807L22_exp190803_MS297_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H064_190807L22_exp190803_MS297_SCD_RAPA-120min_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 H064_190807L22_exp190803_MS297_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H064_190807L22_exp190803_MS297_SCD_RAPA-120min_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 H064_190807L22_exp190803_MS297_SCD_RAPA-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H064_190807L22_exp190803_MS297_SCD_RAPA-120min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H064_190807L22_exp190803_MS297_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H064_190807L22_exp190803_MS297_SCD_RAPA-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H064_190807L22_exp190803_MS297_SCD_RAPA-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H064_190807L22_exp190803_MS297_SCD_RAPA-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H065_190807L23_exp190803_MS250_SCD_DMSO-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H065_190807L23_exp190803_MS250_SCD_DMSO-120min_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 H065_190807L23_exp190803_MS250_SCD_DMSO-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H065_190807L23_exp190803_MS250_SCD_DMSO-120min_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 H065_190807L23_exp190803_MS250_SCD_DMSO-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H065_190807L23_exp190803_MS250_SCD_DMSO-120min_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 H065_190807L23_exp190803_MS250_SCD_DMSO-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H065_190807L23_exp190803_MS250_SCD_DMSO-120min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H065_190807L23_exp190803_MS250_SCD_DMSO-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H065_190807L23_exp190803_MS250_SCD_DMSO-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H065_190807L23_exp190803_MS250_SCD_DMSO-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H065_190807L23_exp190803_MS250_SCD_DMSO-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H066_190807L24_exp190803_MS297_SCD_DMSO-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H066_190807L24_exp190803_MS297_SCD_DMSO-120min_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 H066_190807L24_exp190803_MS297_SCD_DMSO-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H066_190807L24_exp190803_MS297_SCD_DMSO-120min_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 H066_190807L24_exp190803_MS297_SCD_DMSO-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H066_190807L24_exp190803_MS297_SCD_DMSO-120min_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 H066_190807L24_exp190803_MS297_SCD_DMSO-120min_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H066_190807L24_exp190803_MS297_SCD_DMSO-120min_input.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H066_190807L24_exp190803_MS297_SCD_DMSO-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H066_190807L24_exp190803_MS297_SCD_DMSO-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H066_190807L24_exp190803_MS297_SCD_DMSO-120min_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H066_190807L24_exp190803_MS297_SCD_DMSO-120min_input.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.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 H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.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 H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.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 H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H067_190807L49_exp190803_MS250_SCD_DMSO-120min_input_R.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.1x36mers.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 H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.2x36mers.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 H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.2x36mers.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 H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H068_190807L25_exp190803_MS207_SCD_RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.1x36mers.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 H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.2x36mers.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 H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.2x36mers.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 H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H069_190807L26_exp190803_MS249_SCD_RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.1x36mers.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 H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.2x36mers.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 H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.2x36mers.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 H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H070_190807L27_exp190803_MS250_SCD_RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.1x36mers.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 H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.2x36mers.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 H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.2x36mers.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 H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H071_190807L28_exp190803_MS297_SCD_RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.1x36mers.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 H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.2x36mers.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 H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.2x36mers.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 H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H072_190807L29_exp190803_MS250_SCD_DMSO-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.1x36mers.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 H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.2x36mers.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 H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.2x36mers.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 H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H073_190807L30_exp190803_MS297_SCD_DMSO-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.1x36mers.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 H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.2x36mers.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 H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.2x36mers.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 H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H074_190807L31_exp190803_MS207_SCD_RAPA-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.1x36mers.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 H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.2x36mers.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 H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.2x36mers.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 H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H075_190807L32_exp190803_MS249_SCD_RAPA-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.1x36mers.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 H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.2x36mers.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 H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.2x36mers.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 H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H076_190807L33_exp190803_MS250_SCD_RAPA-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.1x36mers.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 H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.2x36mers.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 H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.2x36mers.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 H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H077_190807L34_exp190803_MS297_SCD_RAPA-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.1x36mers.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 H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.2x36mers.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 H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.2x36mers.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 H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H078_190807L35_exp190803_MS250_SCD_DMSO-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.1x36mers.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 H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.2x36mers.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 H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.2x36mers.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 H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H079_190807L36_exp190803_MS297_SCD_DMSO-120min_AB04.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H080_190807L37_exp190803_MS207_SCD_RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H080_190807L37_exp190803_MS207_SCD_RAPA-120min_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 H080_190807L37_exp190803_MS207_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H080_190807L37_exp190803_MS207_SCD_RAPA-120min_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 H080_190807L37_exp190803_MS207_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H080_190807L37_exp190803_MS207_SCD_RAPA-120min_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 H080_190807L37_exp190803_MS207_SCD_RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H080_190807L37_exp190803_MS207_SCD_RAPA-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H080_190807L37_exp190803_MS207_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H080_190807L37_exp190803_MS207_SCD_RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H080_190807L37_exp190803_MS207_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H080_190807L37_exp190803_MS207_SCD_RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H081_190807L38_exp190803_MS249_SCD_RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H081_190807L38_exp190803_MS249_SCD_RAPA-120min_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 H081_190807L38_exp190803_MS249_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H081_190807L38_exp190803_MS249_SCD_RAPA-120min_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 H081_190807L38_exp190803_MS249_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H081_190807L38_exp190803_MS249_SCD_RAPA-120min_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 H081_190807L38_exp190803_MS249_SCD_RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H081_190807L38_exp190803_MS249_SCD_RAPA-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H081_190807L38_exp190803_MS249_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H081_190807L38_exp190803_MS249_SCD_RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H081_190807L38_exp190803_MS249_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H081_190807L38_exp190803_MS249_SCD_RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H082_190807L39_exp190803_MS250_SCD_RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H082_190807L39_exp190803_MS250_SCD_RAPA-120min_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 H082_190807L39_exp190803_MS250_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H082_190807L39_exp190803_MS250_SCD_RAPA-120min_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 H082_190807L39_exp190803_MS250_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H082_190807L39_exp190803_MS250_SCD_RAPA-120min_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 H082_190807L39_exp190803_MS250_SCD_RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H082_190807L39_exp190803_MS250_SCD_RAPA-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H082_190807L39_exp190803_MS250_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H082_190807L39_exp190803_MS250_SCD_RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H082_190807L39_exp190803_MS250_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H082_190807L39_exp190803_MS250_SCD_RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H083_190807L40_exp190803_MS297_SCD_RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H083_190807L40_exp190803_MS297_SCD_RAPA-120min_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 H083_190807L40_exp190803_MS297_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H083_190807L40_exp190803_MS297_SCD_RAPA-120min_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 H083_190807L40_exp190803_MS297_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H083_190807L40_exp190803_MS297_SCD_RAPA-120min_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 H083_190807L40_exp190803_MS297_SCD_RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H083_190807L40_exp190803_MS297_SCD_RAPA-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H083_190807L40_exp190803_MS297_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H083_190807L40_exp190803_MS297_SCD_RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H083_190807L40_exp190803_MS297_SCD_RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H083_190807L40_exp190803_MS297_SCD_RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H084_190807L41_exp190803_MS250_SCD_DMSO-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H084_190807L41_exp190803_MS250_SCD_DMSO-120min_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 H084_190807L41_exp190803_MS250_SCD_DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H084_190807L41_exp190803_MS250_SCD_DMSO-120min_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 H084_190807L41_exp190803_MS250_SCD_DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H084_190807L41_exp190803_MS250_SCD_DMSO-120min_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 H084_190807L41_exp190803_MS250_SCD_DMSO-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H084_190807L41_exp190803_MS250_SCD_DMSO-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H084_190807L41_exp190803_MS250_SCD_DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H084_190807L41_exp190803_MS250_SCD_DMSO-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H084_190807L41_exp190803_MS250_SCD_DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H084_190807L41_exp190803_MS250_SCD_DMSO-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H085_190807L42_exp190803_MS297_SCD_DMSO-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H085_190807L42_exp190803_MS297_SCD_DMSO-120min_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 H085_190807L42_exp190803_MS297_SCD_DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H085_190807L42_exp190803_MS297_SCD_DMSO-120min_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 H085_190807L42_exp190803_MS297_SCD_DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H085_190807L42_exp190803_MS297_SCD_DMSO-120min_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 H085_190807L42_exp190803_MS297_SCD_DMSO-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H085_190807L42_exp190803_MS297_SCD_DMSO-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H085_190807L42_exp190803_MS297_SCD_DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H085_190807L42_exp190803_MS297_SCD_DMSO-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H085_190807L42_exp190803_MS297_SCD_DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H085_190807L42_exp190803_MS297_SCD_DMSO-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.1x36mers.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 H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.2x36mers.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 H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.2x36mers.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 H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H086_190807L43_exp190803_MS207_SCD_RAPA-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.1x36mers.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 H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.2x36mers.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 H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.2x36mers.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 H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H087_190807L44_exp190803_MS249_SCD_RAPA-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.1x36mers.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 H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.2x36mers.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 H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.2x36mers.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 H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H088_190807L45_exp190803_MS250_SCD_RAPA-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.1x36mers.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 H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.2x36mers.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 H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.2x36mers.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 H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H089_190807L46_exp190803_MS297_SCD_RAPA-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.1x36mers.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 H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.2x36mers.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 H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.2x36mers.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 H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H090_190807L47_exp190803_MS250_SCD_DMSO-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.1x36mers.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 H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.2x36mers.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 H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.2x36mers.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 H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H091_190807L48_exp190803_MS297_SCD_DMSO-120min_AB21.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.1x36mers.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 H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.2x36mers.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 H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.2x36mers.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 H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H092_190923L43_exp190803_MS207_SCD-RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.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 H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.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 H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.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 H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H093_190923L79_exp190803_MS207_SCD-RAPA-120min_AB107_R.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.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 H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.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 H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.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 H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H094_190923L44_exp190803_MS249_SCD-RAPA-120min_AB107_R.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.1x36mers.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 H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.2x36mers.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 H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.2x36mers.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 H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H095_190923L80_exp190803_MS249_SCD-RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.1x36mers.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 H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.2x36mers.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 H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.2x36mers.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 H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H096_190923L45_exp190803_MS250_SCD-RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.1x36mers.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 H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.2x36mers.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 H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.2x36mers.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 H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H097_190923L46_exp190803_MS297_SCD-RAPA-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.1x36mers.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 H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.2x36mers.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 H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.2x36mers.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 H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H098_190923L47_exp190803_MS250_SCD-DMSO-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.1x36mers.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 H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.2x36mers.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 H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.2x36mers.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 H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H099_190923L48_exp190803_MS297_SCD-DMSO-120min_AB107.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.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 H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.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 H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.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 H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H100_190923L81_exp190803_MS297_SCD-DMSO-120min_AB107_R.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H101_190923L49_exp190803_MS207_SCD-RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H101_190923L49_exp190803_MS207_SCD-RAPA-120min_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 H101_190923L49_exp190803_MS207_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H101_190923L49_exp190803_MS207_SCD-RAPA-120min_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 H101_190923L49_exp190803_MS207_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H101_190923L49_exp190803_MS207_SCD-RAPA-120min_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 H101_190923L49_exp190803_MS207_SCD-RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H101_190923L49_exp190803_MS207_SCD-RAPA-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H101_190923L49_exp190803_MS207_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H101_190923L49_exp190803_MS207_SCD-RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H101_190923L49_exp190803_MS207_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H101_190923L49_exp190803_MS207_SCD-RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H102_190923L50_exp190803_MS249_SCD-RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H102_190923L50_exp190803_MS249_SCD-RAPA-120min_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 H102_190923L50_exp190803_MS249_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H102_190923L50_exp190803_MS249_SCD-RAPA-120min_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 H102_190923L50_exp190803_MS249_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H102_190923L50_exp190803_MS249_SCD-RAPA-120min_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 H102_190923L50_exp190803_MS249_SCD-RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H102_190923L50_exp190803_MS249_SCD-RAPA-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H102_190923L50_exp190803_MS249_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H102_190923L50_exp190803_MS249_SCD-RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H102_190923L50_exp190803_MS249_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H102_190923L50_exp190803_MS249_SCD-RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H103_190923L51_exp190803_MS250_SCD-RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H103_190923L51_exp190803_MS250_SCD-RAPA-120min_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 H103_190923L51_exp190803_MS250_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H103_190923L51_exp190803_MS250_SCD-RAPA-120min_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 H103_190923L51_exp190803_MS250_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H103_190923L51_exp190803_MS250_SCD-RAPA-120min_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 H103_190923L51_exp190803_MS250_SCD-RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H103_190923L51_exp190803_MS250_SCD-RAPA-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H103_190923L51_exp190803_MS250_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H103_190923L51_exp190803_MS250_SCD-RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H103_190923L51_exp190803_MS250_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H103_190923L51_exp190803_MS250_SCD-RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H104_190923L52_exp190803_MS297_SCD-RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H104_190923L52_exp190803_MS297_SCD-RAPA-120min_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 H104_190923L52_exp190803_MS297_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H104_190923L52_exp190803_MS297_SCD-RAPA-120min_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 H104_190923L52_exp190803_MS297_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H104_190923L52_exp190803_MS297_SCD-RAPA-120min_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 H104_190923L52_exp190803_MS297_SCD-RAPA-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H104_190923L52_exp190803_MS297_SCD-RAPA-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H104_190923L52_exp190803_MS297_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H104_190923L52_exp190803_MS297_SCD-RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H104_190923L52_exp190803_MS297_SCD-RAPA-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H104_190923L52_exp190803_MS297_SCD-RAPA-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H105_190923L53_exp190803_MS250_SCD-DMSO-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H105_190923L53_exp190803_MS250_SCD-DMSO-120min_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 H105_190923L53_exp190803_MS250_SCD-DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H105_190923L53_exp190803_MS250_SCD-DMSO-120min_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 H105_190923L53_exp190803_MS250_SCD-DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H105_190923L53_exp190803_MS250_SCD-DMSO-120min_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 H105_190923L53_exp190803_MS250_SCD-DMSO-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H105_190923L53_exp190803_MS250_SCD-DMSO-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H105_190923L53_exp190803_MS250_SCD-DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H105_190923L53_exp190803_MS250_SCD-DMSO-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H105_190923L53_exp190803_MS250_SCD-DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H105_190923L53_exp190803_MS250_SCD-DMSO-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H106_190923L54_exp190803_MS297_SCD-DMSO-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H106_190923L54_exp190803_MS297_SCD-DMSO-120min_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 H106_190923L54_exp190803_MS297_SCD-DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H106_190923L54_exp190803_MS297_SCD-DMSO-120min_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 H106_190923L54_exp190803_MS297_SCD-DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H106_190923L54_exp190803_MS297_SCD-DMSO-120min_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 H106_190923L54_exp190803_MS297_SCD-DMSO-120min_AB20.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H106_190923L54_exp190803_MS297_SCD-DMSO-120min_AB20.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H106_190923L54_exp190803_MS297_SCD-DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H106_190923L54_exp190803_MS297_SCD-DMSO-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H106_190923L54_exp190803_MS297_SCD-DMSO-120min_AB20.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H106_190923L54_exp190803_MS297_SCD-DMSO-120min_AB20.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.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 H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.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 H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.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 H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam SAMstats-H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.1x36mers.Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam SAMstats-H107_190923L82_exp190803_MS207_SCD-RAPA-120min_AB20_R.2x36mers.Schizosaccharomyces_pombe.ASM294v2.20.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.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 J001_201116L01_exp201101_MS625_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J001_201116L01_exp201101_MS625_SCD_ATC-45min_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 J001_201116L01_exp201101_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J001_201116L01_exp201101_MS625_SCD_ATC-45min_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 J001_201116L01_exp201101_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J001_201116L01_exp201101_MS625_SCD_ATC-45min_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 J001_201116L01_exp201101_MS625_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J001_201116L01_exp201101_MS625_SCD_ATC-45min_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 J001_201116L01_exp201101_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J001_201116L01_exp201101_MS625_SCD_ATC-45min_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 J001_201116L01_exp201101_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J001_201116L01_exp201101_MS625_SCD_ATC-45min_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 J002_201116L02_exp201101_MS626_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J002_201116L02_exp201101_MS626_SCD_ATC-45min_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 J002_201116L02_exp201101_MS626_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J002_201116L02_exp201101_MS626_SCD_ATC-45min_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 J002_201116L02_exp201101_MS626_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J002_201116L02_exp201101_MS626_SCD_ATC-45min_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 J002_201116L02_exp201101_MS626_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J002_201116L02_exp201101_MS626_SCD_ATC-45min_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 J002_201116L02_exp201101_MS626_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J002_201116L02_exp201101_MS626_SCD_ATC-45min_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 J002_201116L02_exp201101_MS626_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J002_201116L02_exp201101_MS626_SCD_ATC-45min_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 J003_201116L03_exp201101_MS628_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J003_201116L03_exp201101_MS628_SCD_ATC-45min_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 J003_201116L03_exp201101_MS628_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J003_201116L03_exp201101_MS628_SCD_ATC-45min_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 J003_201116L03_exp201101_MS628_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J003_201116L03_exp201101_MS628_SCD_ATC-45min_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 J003_201116L03_exp201101_MS628_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J003_201116L03_exp201101_MS628_SCD_ATC-45min_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 J003_201116L03_exp201101_MS628_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J003_201116L03_exp201101_MS628_SCD_ATC-45min_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 J003_201116L03_exp201101_MS628_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J003_201116L03_exp201101_MS628_SCD_ATC-45min_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 J004_201116L04_exp201101_MS629_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J004_201116L04_exp201101_MS629_SCD_ATC-45min_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 J004_201116L04_exp201101_MS629_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J004_201116L04_exp201101_MS629_SCD_ATC-45min_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 J004_201116L04_exp201101_MS629_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J004_201116L04_exp201101_MS629_SCD_ATC-45min_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 J004_201116L04_exp201101_MS629_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J004_201116L04_exp201101_MS629_SCD_ATC-45min_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 J004_201116L04_exp201101_MS629_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J004_201116L04_exp201101_MS629_SCD_ATC-45min_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 J004_201116L04_exp201101_MS629_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J004_201116L04_exp201101_MS629_SCD_ATC-45min_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 J005_201116L05_exp201101_MS630_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J005_201116L05_exp201101_MS630_SCD_ATC-45min_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 J005_201116L05_exp201101_MS630_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J005_201116L05_exp201101_MS630_SCD_ATC-45min_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 J005_201116L05_exp201101_MS630_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J005_201116L05_exp201101_MS630_SCD_ATC-45min_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 J005_201116L05_exp201101_MS630_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J005_201116L05_exp201101_MS630_SCD_ATC-45min_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 J005_201116L05_exp201101_MS630_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J005_201116L05_exp201101_MS630_SCD_ATC-45min_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 J005_201116L05_exp201101_MS630_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J005_201116L05_exp201101_MS630_SCD_ATC-45min_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 J006_201116L06_exp201101_MS205_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J006_201116L06_exp201101_MS205_SCD_RAPA-65min_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 J006_201116L06_exp201101_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J006_201116L06_exp201101_MS205_SCD_RAPA-65min_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 J006_201116L06_exp201101_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J006_201116L06_exp201101_MS205_SCD_RAPA-65min_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 J006_201116L06_exp201101_MS205_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J006_201116L06_exp201101_MS205_SCD_RAPA-65min_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 J006_201116L06_exp201101_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J006_201116L06_exp201101_MS205_SCD_RAPA-65min_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 J006_201116L06_exp201101_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J006_201116L06_exp201101_MS205_SCD_RAPA-65min_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 J007_201116L07_exp201102_MS625_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J007_201116L07_exp201102_MS625_SCD_ATC-45min_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 J007_201116L07_exp201102_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J007_201116L07_exp201102_MS625_SCD_ATC-45min_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 J007_201116L07_exp201102_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J007_201116L07_exp201102_MS625_SCD_ATC-45min_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 J007_201116L07_exp201102_MS625_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J007_201116L07_exp201102_MS625_SCD_ATC-45min_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 J007_201116L07_exp201102_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J007_201116L07_exp201102_MS625_SCD_ATC-45min_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 J007_201116L07_exp201102_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J007_201116L07_exp201102_MS625_SCD_ATC-45min_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 J008_201116L08_exp201102_MS631_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J008_201116L08_exp201102_MS631_SCD_ATC-45min_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 J008_201116L08_exp201102_MS631_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J008_201116L08_exp201102_MS631_SCD_ATC-45min_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 J008_201116L08_exp201102_MS631_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J008_201116L08_exp201102_MS631_SCD_ATC-45min_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 J008_201116L08_exp201102_MS631_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J008_201116L08_exp201102_MS631_SCD_ATC-45min_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 J008_201116L08_exp201102_MS631_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J008_201116L08_exp201102_MS631_SCD_ATC-45min_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 J008_201116L08_exp201102_MS631_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J008_201116L08_exp201102_MS631_SCD_ATC-45min_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 J009_201116L09_exp201102_MS632_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J009_201116L09_exp201102_MS632_SCD_ATC-45min_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 J009_201116L09_exp201102_MS632_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J009_201116L09_exp201102_MS632_SCD_ATC-45min_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 J009_201116L09_exp201102_MS632_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J009_201116L09_exp201102_MS632_SCD_ATC-45min_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 J009_201116L09_exp201102_MS632_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J009_201116L09_exp201102_MS632_SCD_ATC-45min_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 J009_201116L09_exp201102_MS632_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J009_201116L09_exp201102_MS632_SCD_ATC-45min_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 J009_201116L09_exp201102_MS632_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J009_201116L09_exp201102_MS632_SCD_ATC-45min_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 J010_201116L10_exp201102_MS633_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J010_201116L10_exp201102_MS633_SCD_ATC-45min_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 J010_201116L10_exp201102_MS633_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J010_201116L10_exp201102_MS633_SCD_ATC-45min_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 J010_201116L10_exp201102_MS633_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J010_201116L10_exp201102_MS633_SCD_ATC-45min_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 J010_201116L10_exp201102_MS633_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J010_201116L10_exp201102_MS633_SCD_ATC-45min_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 J010_201116L10_exp201102_MS633_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J010_201116L10_exp201102_MS633_SCD_ATC-45min_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 J010_201116L10_exp201102_MS633_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J010_201116L10_exp201102_MS633_SCD_ATC-45min_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 J011_201116L11_exp201102_MS636_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J011_201116L11_exp201102_MS636_SCD_ATC-45min_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 J011_201116L11_exp201102_MS636_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J011_201116L11_exp201102_MS636_SCD_ATC-45min_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 J011_201116L11_exp201102_MS636_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J011_201116L11_exp201102_MS636_SCD_ATC-45min_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 J011_201116L11_exp201102_MS636_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J011_201116L11_exp201102_MS636_SCD_ATC-45min_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 J011_201116L11_exp201102_MS636_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J011_201116L11_exp201102_MS636_SCD_ATC-45min_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 J011_201116L11_exp201102_MS636_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J011_201116L11_exp201102_MS636_SCD_ATC-45min_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 J012_201116L12_exp201102_MS205_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J012_201116L12_exp201102_MS205_SCD_RAPA-65min_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 J012_201116L12_exp201102_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J012_201116L12_exp201102_MS205_SCD_RAPA-65min_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 J012_201116L12_exp201102_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J012_201116L12_exp201102_MS205_SCD_RAPA-65min_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 J012_201116L12_exp201102_MS205_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J012_201116L12_exp201102_MS205_SCD_RAPA-65min_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 J012_201116L12_exp201102_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J012_201116L12_exp201102_MS205_SCD_RAPA-65min_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 J012_201116L12_exp201102_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J012_201116L12_exp201102_MS205_SCD_RAPA-65min_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 J013_201116L13_exp201102_MS625_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J013_201116L13_exp201102_MS625_SCD_ATC-45min_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 J013_201116L13_exp201102_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J013_201116L13_exp201102_MS625_SCD_ATC-45min_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 J013_201116L13_exp201102_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J013_201116L13_exp201102_MS625_SCD_ATC-45min_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 J013_201116L13_exp201102_MS625_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J013_201116L13_exp201102_MS625_SCD_ATC-45min_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 J013_201116L13_exp201102_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J013_201116L13_exp201102_MS625_SCD_ATC-45min_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 J013_201116L13_exp201102_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J013_201116L13_exp201102_MS625_SCD_ATC-45min_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 J014_201116L14_exp201102_MS634_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J014_201116L14_exp201102_MS634_SCD_ATC-45min_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 J014_201116L14_exp201102_MS634_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J014_201116L14_exp201102_MS634_SCD_ATC-45min_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 J014_201116L14_exp201102_MS634_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J014_201116L14_exp201102_MS634_SCD_ATC-45min_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 J014_201116L14_exp201102_MS634_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J014_201116L14_exp201102_MS634_SCD_ATC-45min_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 J014_201116L14_exp201102_MS634_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J014_201116L14_exp201102_MS634_SCD_ATC-45min_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 J014_201116L14_exp201102_MS634_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J014_201116L14_exp201102_MS634_SCD_ATC-45min_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 J015_201116L15_exp201102_MS635_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J015_201116L15_exp201102_MS635_SCD_ATC-45min_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 J015_201116L15_exp201102_MS635_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J015_201116L15_exp201102_MS635_SCD_ATC-45min_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 J015_201116L15_exp201102_MS635_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J015_201116L15_exp201102_MS635_SCD_ATC-45min_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 J015_201116L15_exp201102_MS635_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J015_201116L15_exp201102_MS635_SCD_ATC-45min_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 J015_201116L15_exp201102_MS635_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J015_201116L15_exp201102_MS635_SCD_ATC-45min_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 J015_201116L15_exp201102_MS635_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J015_201116L15_exp201102_MS635_SCD_ATC-45min_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 J016_201116L16_exp201102_MS638_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J016_201116L16_exp201102_MS638_SCD_ATC-45min_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 J016_201116L16_exp201102_MS638_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J016_201116L16_exp201102_MS638_SCD_ATC-45min_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 J016_201116L16_exp201102_MS638_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J016_201116L16_exp201102_MS638_SCD_ATC-45min_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 J016_201116L16_exp201102_MS638_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J016_201116L16_exp201102_MS638_SCD_ATC-45min_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 J016_201116L16_exp201102_MS638_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J016_201116L16_exp201102_MS638_SCD_ATC-45min_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 J016_201116L16_exp201102_MS638_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J016_201116L16_exp201102_MS638_SCD_ATC-45min_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 J017_201116L17_exp201102_MS641_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J017_201116L17_exp201102_MS641_SCD_ATC-45min_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 J017_201116L17_exp201102_MS641_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J017_201116L17_exp201102_MS641_SCD_ATC-45min_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 J017_201116L17_exp201102_MS641_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J017_201116L17_exp201102_MS641_SCD_ATC-45min_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 J017_201116L17_exp201102_MS641_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J017_201116L17_exp201102_MS641_SCD_ATC-45min_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 J017_201116L17_exp201102_MS641_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J017_201116L17_exp201102_MS641_SCD_ATC-45min_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 J017_201116L17_exp201102_MS641_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J017_201116L17_exp201102_MS641_SCD_ATC-45min_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 J018_201116L18_exp201102_MS648_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J018_201116L18_exp201102_MS648_SCD_ATC-45min_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 J018_201116L18_exp201102_MS648_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J018_201116L18_exp201102_MS648_SCD_ATC-45min_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 J018_201116L18_exp201102_MS648_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J018_201116L18_exp201102_MS648_SCD_ATC-45min_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 J018_201116L18_exp201102_MS648_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J018_201116L18_exp201102_MS648_SCD_ATC-45min_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 J018_201116L18_exp201102_MS648_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J018_201116L18_exp201102_MS648_SCD_ATC-45min_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 J018_201116L18_exp201102_MS648_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J018_201116L18_exp201102_MS648_SCD_ATC-45min_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 J019_201116L19_exp201102_MS205_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J019_201116L19_exp201102_MS205_SCD_RAPA-65min_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 J019_201116L19_exp201102_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J019_201116L19_exp201102_MS205_SCD_RAPA-65min_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 J019_201116L19_exp201102_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J019_201116L19_exp201102_MS205_SCD_RAPA-65min_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 J019_201116L19_exp201102_MS205_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J019_201116L19_exp201102_MS205_SCD_RAPA-65min_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 J019_201116L19_exp201102_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J019_201116L19_exp201102_MS205_SCD_RAPA-65min_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 J019_201116L19_exp201102_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J019_201116L19_exp201102_MS205_SCD_RAPA-65min_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 J020_201116L20_exp201101_MS625_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J020_201116L20_exp201101_MS625_SCD_ATC-45min_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 J020_201116L20_exp201101_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J020_201116L20_exp201101_MS625_SCD_ATC-45min_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 J020_201116L20_exp201101_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J020_201116L20_exp201101_MS625_SCD_ATC-45min_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 J020_201116L20_exp201101_MS625_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J020_201116L20_exp201101_MS625_SCD_ATC-45min_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 J020_201116L20_exp201101_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J020_201116L20_exp201101_MS625_SCD_ATC-45min_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 J020_201116L20_exp201101_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J020_201116L20_exp201101_MS625_SCD_ATC-45min_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 J021_201116L21_exp201101_MS626_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J021_201116L21_exp201101_MS626_SCD_ATC-45min_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 J021_201116L21_exp201101_MS626_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J021_201116L21_exp201101_MS626_SCD_ATC-45min_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 J021_201116L21_exp201101_MS626_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J021_201116L21_exp201101_MS626_SCD_ATC-45min_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 J021_201116L21_exp201101_MS626_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J021_201116L21_exp201101_MS626_SCD_ATC-45min_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 J021_201116L21_exp201101_MS626_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J021_201116L21_exp201101_MS626_SCD_ATC-45min_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 J021_201116L21_exp201101_MS626_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J021_201116L21_exp201101_MS626_SCD_ATC-45min_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 J022_201116L22_exp201101_MS628_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J022_201116L22_exp201101_MS628_SCD_ATC-45min_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 J022_201116L22_exp201101_MS628_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J022_201116L22_exp201101_MS628_SCD_ATC-45min_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 J022_201116L22_exp201101_MS628_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J022_201116L22_exp201101_MS628_SCD_ATC-45min_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 J022_201116L22_exp201101_MS628_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J022_201116L22_exp201101_MS628_SCD_ATC-45min_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 J022_201116L22_exp201101_MS628_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J022_201116L22_exp201101_MS628_SCD_ATC-45min_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 J022_201116L22_exp201101_MS628_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J022_201116L22_exp201101_MS628_SCD_ATC-45min_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 J023_201116L23_exp201101_MS629_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J023_201116L23_exp201101_MS629_SCD_ATC-45min_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 J023_201116L23_exp201101_MS629_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J023_201116L23_exp201101_MS629_SCD_ATC-45min_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 J023_201116L23_exp201101_MS629_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J023_201116L23_exp201101_MS629_SCD_ATC-45min_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 J023_201116L23_exp201101_MS629_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J023_201116L23_exp201101_MS629_SCD_ATC-45min_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 J023_201116L23_exp201101_MS629_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J023_201116L23_exp201101_MS629_SCD_ATC-45min_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 J023_201116L23_exp201101_MS629_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J023_201116L23_exp201101_MS629_SCD_ATC-45min_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 J024_201116L24_exp201101_MS630_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J024_201116L24_exp201101_MS630_SCD_ATC-45min_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 J024_201116L24_exp201101_MS630_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J024_201116L24_exp201101_MS630_SCD_ATC-45min_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 J024_201116L24_exp201101_MS630_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J024_201116L24_exp201101_MS630_SCD_ATC-45min_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 J024_201116L24_exp201101_MS630_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J024_201116L24_exp201101_MS630_SCD_ATC-45min_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 J024_201116L24_exp201101_MS630_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J024_201116L24_exp201101_MS630_SCD_ATC-45min_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 J024_201116L24_exp201101_MS630_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J024_201116L24_exp201101_MS630_SCD_ATC-45min_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 J025_201116L25_exp201101_MS205_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J025_201116L25_exp201101_MS205_SCD_RAPA-65min_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 J025_201116L25_exp201101_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J025_201116L25_exp201101_MS205_SCD_RAPA-65min_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 J025_201116L25_exp201101_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J025_201116L25_exp201101_MS205_SCD_RAPA-65min_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 J025_201116L25_exp201101_MS205_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J025_201116L25_exp201101_MS205_SCD_RAPA-65min_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 J025_201116L25_exp201101_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J025_201116L25_exp201101_MS205_SCD_RAPA-65min_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 J025_201116L25_exp201101_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J025_201116L25_exp201101_MS205_SCD_RAPA-65min_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 J026_201116L26_exp201102_MS625_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J026_201116L26_exp201102_MS625_SCD_ATC-45min_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 J026_201116L26_exp201102_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J026_201116L26_exp201102_MS625_SCD_ATC-45min_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 J026_201116L26_exp201102_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J026_201116L26_exp201102_MS625_SCD_ATC-45min_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 J026_201116L26_exp201102_MS625_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J026_201116L26_exp201102_MS625_SCD_ATC-45min_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 J026_201116L26_exp201102_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J026_201116L26_exp201102_MS625_SCD_ATC-45min_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 J026_201116L26_exp201102_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J026_201116L26_exp201102_MS625_SCD_ATC-45min_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 J027_201116L27_exp201102_MS631_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J027_201116L27_exp201102_MS631_SCD_ATC-45min_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 J027_201116L27_exp201102_MS631_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J027_201116L27_exp201102_MS631_SCD_ATC-45min_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 J027_201116L27_exp201102_MS631_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J027_201116L27_exp201102_MS631_SCD_ATC-45min_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 J027_201116L27_exp201102_MS631_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J027_201116L27_exp201102_MS631_SCD_ATC-45min_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 J027_201116L27_exp201102_MS631_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J027_201116L27_exp201102_MS631_SCD_ATC-45min_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 J027_201116L27_exp201102_MS631_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J027_201116L27_exp201102_MS631_SCD_ATC-45min_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 J028_201116L28_exp201102_MS632_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J028_201116L28_exp201102_MS632_SCD_ATC-45min_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 J028_201116L28_exp201102_MS632_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J028_201116L28_exp201102_MS632_SCD_ATC-45min_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 J028_201116L28_exp201102_MS632_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J028_201116L28_exp201102_MS632_SCD_ATC-45min_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 J028_201116L28_exp201102_MS632_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J028_201116L28_exp201102_MS632_SCD_ATC-45min_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 J028_201116L28_exp201102_MS632_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J028_201116L28_exp201102_MS632_SCD_ATC-45min_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 J028_201116L28_exp201102_MS632_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J028_201116L28_exp201102_MS632_SCD_ATC-45min_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 J029_201116L29_exp201102_MS633_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J029_201116L29_exp201102_MS633_SCD_ATC-45min_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 J029_201116L29_exp201102_MS633_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J029_201116L29_exp201102_MS633_SCD_ATC-45min_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 J029_201116L29_exp201102_MS633_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J029_201116L29_exp201102_MS633_SCD_ATC-45min_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 J029_201116L29_exp201102_MS633_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J029_201116L29_exp201102_MS633_SCD_ATC-45min_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 J029_201116L29_exp201102_MS633_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J029_201116L29_exp201102_MS633_SCD_ATC-45min_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 J029_201116L29_exp201102_MS633_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J029_201116L29_exp201102_MS633_SCD_ATC-45min_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 J030_201116L30_exp201102_MS636_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J030_201116L30_exp201102_MS636_SCD_ATC-45min_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 J030_201116L30_exp201102_MS636_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J030_201116L30_exp201102_MS636_SCD_ATC-45min_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 J030_201116L30_exp201102_MS636_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J030_201116L30_exp201102_MS636_SCD_ATC-45min_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 J030_201116L30_exp201102_MS636_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J030_201116L30_exp201102_MS636_SCD_ATC-45min_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 J030_201116L30_exp201102_MS636_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J030_201116L30_exp201102_MS636_SCD_ATC-45min_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 J030_201116L30_exp201102_MS636_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J030_201116L30_exp201102_MS636_SCD_ATC-45min_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 J031_201116L31_exp201102_MS205_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J031_201116L31_exp201102_MS205_SCD_RAPA-65min_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 J031_201116L31_exp201102_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J031_201116L31_exp201102_MS205_SCD_RAPA-65min_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 J031_201116L31_exp201102_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J031_201116L31_exp201102_MS205_SCD_RAPA-65min_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 J031_201116L31_exp201102_MS205_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J031_201116L31_exp201102_MS205_SCD_RAPA-65min_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 J031_201116L31_exp201102_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J031_201116L31_exp201102_MS205_SCD_RAPA-65min_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 J031_201116L31_exp201102_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J031_201116L31_exp201102_MS205_SCD_RAPA-65min_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 J032_201116L32_exp201102_MS625_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J032_201116L32_exp201102_MS625_SCD_ATC-45min_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 J032_201116L32_exp201102_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J032_201116L32_exp201102_MS625_SCD_ATC-45min_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 J032_201116L32_exp201102_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J032_201116L32_exp201102_MS625_SCD_ATC-45min_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 J032_201116L32_exp201102_MS625_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J032_201116L32_exp201102_MS625_SCD_ATC-45min_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 J032_201116L32_exp201102_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J032_201116L32_exp201102_MS625_SCD_ATC-45min_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 J032_201116L32_exp201102_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J032_201116L32_exp201102_MS625_SCD_ATC-45min_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 J033_201116L33_exp201102_MS634_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J033_201116L33_exp201102_MS634_SCD_ATC-45min_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 J033_201116L33_exp201102_MS634_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J033_201116L33_exp201102_MS634_SCD_ATC-45min_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 J033_201116L33_exp201102_MS634_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J033_201116L33_exp201102_MS634_SCD_ATC-45min_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 J033_201116L33_exp201102_MS634_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J033_201116L33_exp201102_MS634_SCD_ATC-45min_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 J033_201116L33_exp201102_MS634_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J033_201116L33_exp201102_MS634_SCD_ATC-45min_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 J033_201116L33_exp201102_MS634_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J033_201116L33_exp201102_MS634_SCD_ATC-45min_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 J034_201116L34_exp201102_MS635_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J034_201116L34_exp201102_MS635_SCD_ATC-45min_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 J034_201116L34_exp201102_MS635_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J034_201116L34_exp201102_MS635_SCD_ATC-45min_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 J034_201116L34_exp201102_MS635_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J034_201116L34_exp201102_MS635_SCD_ATC-45min_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 J034_201116L34_exp201102_MS635_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J034_201116L34_exp201102_MS635_SCD_ATC-45min_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 J034_201116L34_exp201102_MS635_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J034_201116L34_exp201102_MS635_SCD_ATC-45min_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 J034_201116L34_exp201102_MS635_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J034_201116L34_exp201102_MS635_SCD_ATC-45min_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 J035_201116L35_exp201102_MS638_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J035_201116L35_exp201102_MS638_SCD_ATC-45min_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 J035_201116L35_exp201102_MS638_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J035_201116L35_exp201102_MS638_SCD_ATC-45min_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 J035_201116L35_exp201102_MS638_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J035_201116L35_exp201102_MS638_SCD_ATC-45min_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 J035_201116L35_exp201102_MS638_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J035_201116L35_exp201102_MS638_SCD_ATC-45min_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 J035_201116L35_exp201102_MS638_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J035_201116L35_exp201102_MS638_SCD_ATC-45min_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 J035_201116L35_exp201102_MS638_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J035_201116L35_exp201102_MS638_SCD_ATC-45min_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 J036_201116L36_exp201102_MS641_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J036_201116L36_exp201102_MS641_SCD_ATC-45min_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 J036_201116L36_exp201102_MS641_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J036_201116L36_exp201102_MS641_SCD_ATC-45min_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 J036_201116L36_exp201102_MS641_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J036_201116L36_exp201102_MS641_SCD_ATC-45min_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 J036_201116L36_exp201102_MS641_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J036_201116L36_exp201102_MS641_SCD_ATC-45min_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 J036_201116L36_exp201102_MS641_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J036_201116L36_exp201102_MS641_SCD_ATC-45min_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 J036_201116L36_exp201102_MS641_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J036_201116L36_exp201102_MS641_SCD_ATC-45min_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 J037_201116L37_exp201102_MS648_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J037_201116L37_exp201102_MS648_SCD_ATC-45min_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 J037_201116L37_exp201102_MS648_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J037_201116L37_exp201102_MS648_SCD_ATC-45min_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 J037_201116L37_exp201102_MS648_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J037_201116L37_exp201102_MS648_SCD_ATC-45min_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 J037_201116L37_exp201102_MS648_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J037_201116L37_exp201102_MS648_SCD_ATC-45min_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 J037_201116L37_exp201102_MS648_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J037_201116L37_exp201102_MS648_SCD_ATC-45min_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 J037_201116L37_exp201102_MS648_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J037_201116L37_exp201102_MS648_SCD_ATC-45min_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 J038_201116L38_exp201102_MS205_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J038_201116L38_exp201102_MS205_SCD_RAPA-65min_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 J038_201116L38_exp201102_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J038_201116L38_exp201102_MS205_SCD_RAPA-65min_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 J038_201116L38_exp201102_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J038_201116L38_exp201102_MS205_SCD_RAPA-65min_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 J038_201116L38_exp201102_MS205_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J038_201116L38_exp201102_MS205_SCD_RAPA-65min_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 J038_201116L38_exp201102_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J038_201116L38_exp201102_MS205_SCD_RAPA-65min_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 J038_201116L38_exp201102_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J038_201116L38_exp201102_MS205_SCD_RAPA-65min_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 J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J039_210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J040_210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J041_210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J042_210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J043_210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J044_210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 J045_210128L21_exp210122_MS205_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J045_210128L21_exp210122_MS205_SCD_RAPA-60min_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 J045_210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J045_210128L21_exp210122_MS205_SCD_RAPA-60min_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 J045_210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J045_210128L21_exp210122_MS205_SCD_RAPA-60min_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 J045_210128L21_exp210122_MS205_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J045_210128L21_exp210122_MS205_SCD_RAPA-60min_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 J045_210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J045_210128L21_exp210122_MS205_SCD_RAPA-60min_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 J045_210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J045_210128L21_exp210122_MS205_SCD_RAPA-60min_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 J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J046_210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J047_210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J048_210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J049_210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J050_210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J051_210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 J052_210128L28_exp210122_MS205_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J052_210128L28_exp210122_MS205_SCD_RAPA-60min_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 J052_210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J052_210128L28_exp210122_MS205_SCD_RAPA-60min_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 J052_210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J052_210128L28_exp210122_MS205_SCD_RAPA-60min_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 J052_210128L28_exp210122_MS205_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J052_210128L28_exp210122_MS205_SCD_RAPA-60min_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 J052_210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J052_210128L28_exp210122_MS205_SCD_RAPA-60min_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 J052_210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J052_210128L28_exp210122_MS205_SCD_RAPA-60min_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 J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J053_210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J054_210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J055_210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J056_210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J057_210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J058_210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 J059_210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J059_210128L07_exp210122_MS205_SCD_RAPA-60min_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 J059_210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J059_210128L07_exp210122_MS205_SCD_RAPA-60min_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 J059_210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J059_210128L07_exp210122_MS205_SCD_RAPA-60min_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 J059_210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J059_210128L07_exp210122_MS205_SCD_RAPA-60min_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 J059_210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J059_210128L07_exp210122_MS205_SCD_RAPA-60min_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 J059_210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J059_210128L07_exp210122_MS205_SCD_RAPA-60min_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 J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J060_210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J061_210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J062_210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J063_210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J064_210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J065_210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 J066_210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J066_210128L14_exp210122_MS205_SCD_RAPA-60min_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 J066_210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J066_210128L14_exp210122_MS205_SCD_RAPA-60min_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 J066_210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J066_210128L14_exp210122_MS205_SCD_RAPA-60min_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 J066_210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J066_210128L14_exp210122_MS205_SCD_RAPA-60min_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 J066_210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J066_210128L14_exp210122_MS205_SCD_RAPA-60min_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 J066_210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J066_210128L14_exp210122_MS205_SCD_RAPA-60min_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 J067_210325L01_exp210314_MS698_SCD_EtOH-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J067_210325L01_exp210314_MS698_SCD_EtOH-45min_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 J067_210325L01_exp210314_MS698_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J067_210325L01_exp210314_MS698_SCD_EtOH-45min_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 J067_210325L01_exp210314_MS698_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J067_210325L01_exp210314_MS698_SCD_EtOH-45min_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 J067_210325L01_exp210314_MS698_SCD_EtOH-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J067_210325L01_exp210314_MS698_SCD_EtOH-45min_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 J067_210325L01_exp210314_MS698_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J067_210325L01_exp210314_MS698_SCD_EtOH-45min_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 J067_210325L01_exp210314_MS698_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J067_210325L01_exp210314_MS698_SCD_EtOH-45min_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 J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_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 J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_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 J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_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 J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_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 J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_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 J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J068_210325L02_exp210314_MS698_SCD_50-ATC-45min_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 J069_210325L03_exp210314_MS214_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J069_210325L03_exp210314_MS214_SCD_RAPA-60min_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 J069_210325L03_exp210314_MS214_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J069_210325L03_exp210314_MS214_SCD_RAPA-60min_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 J069_210325L03_exp210314_MS214_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J069_210325L03_exp210314_MS214_SCD_RAPA-60min_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 J069_210325L03_exp210314_MS214_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J069_210325L03_exp210314_MS214_SCD_RAPA-60min_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 J069_210325L03_exp210314_MS214_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J069_210325L03_exp210314_MS214_SCD_RAPA-60min_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 J069_210325L03_exp210314_MS214_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J069_210325L03_exp210314_MS214_SCD_RAPA-60min_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 J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_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 J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_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 J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_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 J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_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 J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_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 J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J070_210325L04_exp210314_MS698_SCGE_EtOH-70min_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 J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_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 J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_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 J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_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 J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_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 J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_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 J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J071_210325L05_exp210314_MS698_SCGE_50-ATC-70min_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 J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_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 J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_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 J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_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 J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_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 J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_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 J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J072_210325L06_exp210314_MS214_SCGE_RAPA-90min_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 J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_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 J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_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 J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_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 J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_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 J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_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 J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J073_210325L07_exp210314_MS698_SCD_EtOH-45min_IS_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 J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_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 J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_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 J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_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 J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_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 J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_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 J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J074_210325L08_exp210314_MS698_SCD_50-ATC-45min_IS_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 J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_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 J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_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 J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_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 J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_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 J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_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 J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J075_210325L09_exp210314_MS214_SCD_RAPA-60min_IS_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 J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_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 J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_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 J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_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 J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_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 J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_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 J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J076_210325L10_exp210314_MS698_SCGE_EtOH-70min_IS_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 J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J077_210325L11_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_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 J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_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 J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_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 J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_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 J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_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 J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J078_210325L12_exp210314_MS214_SCGE_RAPA-90min_IS_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 J079_210325L19_exp210314_MS698_SCD_EtOH-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J079_210325L19_exp210314_MS698_SCD_EtOH-45min_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 J079_210325L19_exp210314_MS698_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J079_210325L19_exp210314_MS698_SCD_EtOH-45min_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 J079_210325L19_exp210314_MS698_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J079_210325L19_exp210314_MS698_SCD_EtOH-45min_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 J079_210325L19_exp210314_MS698_SCD_EtOH-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J079_210325L19_exp210314_MS698_SCD_EtOH-45min_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 J079_210325L19_exp210314_MS698_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J079_210325L19_exp210314_MS698_SCD_EtOH-45min_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 J079_210325L19_exp210314_MS698_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J079_210325L19_exp210314_MS698_SCD_EtOH-45min_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 J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_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 J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_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 J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_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 J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_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 J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_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 J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J080_210325L20_exp210314_MS698_SCD_50-ATC-45min_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 J081_210325L21_exp210314_MS214_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J081_210325L21_exp210314_MS214_SCD_RAPA-60min_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 J081_210325L21_exp210314_MS214_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J081_210325L21_exp210314_MS214_SCD_RAPA-60min_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 J081_210325L21_exp210314_MS214_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J081_210325L21_exp210314_MS214_SCD_RAPA-60min_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 J081_210325L21_exp210314_MS214_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J081_210325L21_exp210314_MS214_SCD_RAPA-60min_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 J081_210325L21_exp210314_MS214_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J081_210325L21_exp210314_MS214_SCD_RAPA-60min_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 J081_210325L21_exp210314_MS214_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J081_210325L21_exp210314_MS214_SCD_RAPA-60min_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 J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_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 J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_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 J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_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 J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_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 J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_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 J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J082_210325L22_exp210314_MS698_SCGE_EtOH-70min_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 J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_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 J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_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 J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_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 J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_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 J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_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 J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J083_210325L23_exp210314_MS698_SCGE_50-ATC-70min_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 J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_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 J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_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 J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_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 J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_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 J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_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 J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J084_210325L24_exp210314_MS214_SCGE_RAPA-90min_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 J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_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 J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_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 J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_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 J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_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 J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_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 J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J085_210325L25_exp210314_MS698_SCD_EtOH-45min_IS_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 J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_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 J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_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 J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_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 J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_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 J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_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 J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J086_210325L26_exp210314_MS698_SCD_50-ATC-45min_IS_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 J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_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 J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_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 J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_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 J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_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 J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_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 J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J087_210325L27_exp210314_MS214_SCD_RAPA-60min_IS_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 J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_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 J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_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 J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_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 J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_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 J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_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 J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J088_210325L28_exp210314_MS698_SCGE_EtOH-70min_IS_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 J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J089_210325L29_exp210314_MS698_SCGE_50-ATC-70min_IS_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 J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_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 J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_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 J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_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 J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam SAMstats-J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_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 J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_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 J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam SAMstats-J090_210325L30_exp210314_MS214_SCGE_RAPA-90min_IS_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