python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L01_exp230501_A1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L01_exp230501_A1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L01_exp230501_A1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L01_exp230501_A1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L01_exp230501_A1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L01_exp230501_A1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L01_exp230501_A1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L01_exp230501_A1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L02_exp230501_A2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L02_exp230501_A2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L02_exp230501_A2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L02_exp230501_A2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L02_exp230501_A2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L02_exp230501_A2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L02_exp230501_A2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L02_exp230501_A2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L03_exp230501_A3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L03_exp230501_A3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L03_exp230501_A3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L03_exp230501_A3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L03_exp230501_A3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L03_exp230501_A3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L03_exp230501_A3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L03_exp230501_A3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L04_exp230501_A4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L04_exp230501_A4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L04_exp230501_A4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L04_exp230501_A4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L04_exp230501_A4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L04_exp230501_A4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L04_exp230501_A4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L04_exp230501_A4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L05_exp230502_B1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L05_exp230502_B1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L05_exp230502_B1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L05_exp230502_B1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L05_exp230502_B1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L05_exp230502_B1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L05_exp230502_B1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L05_exp230502_B1_CJW7357_060min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L06_exp230502_B2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L06_exp230502_B2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L06_exp230502_B2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L06_exp230502_B2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L06_exp230502_B2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L06_exp230502_B2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L06_exp230502_B2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L06_exp230502_B2_CJW7357_120min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L07_exp230502_B3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L07_exp230502_B3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L07_exp230502_B3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L07_exp230502_B3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L07_exp230502_B3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L07_exp230502_B3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L07_exp230502_B3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L07_exp230502_B3_CJW7357_200min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L08_exp230502_B4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L08_exp230502_B4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L08_exp230502_B4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L08_exp230502_B4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L08_exp230502_B4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L08_exp230502_B4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L08_exp230502_B4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L08_exp230502_B4_CJW7357_240min-arrest_RNA-rRNAdep.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L17_exp230501_A1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L17_exp230501_A1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L17_exp230501_A1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L17_exp230501_A1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L17_exp230501_A1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L17_exp230501_A1_CJW7357_060min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L17_exp230501_A1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L17_exp230501_A1_CJW7357_060min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L18_exp230501_A2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L18_exp230501_A2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L18_exp230501_A2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L18_exp230501_A2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L18_exp230501_A2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L18_exp230501_A2_CJW7357_120min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L18_exp230501_A2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L18_exp230501_A2_CJW7357_120min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L19_exp230501_A3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L19_exp230501_A3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L19_exp230501_A3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L19_exp230501_A3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L19_exp230501_A3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L19_exp230501_A3_CJW7357_200min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L19_exp230501_A3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L19_exp230501_A3_CJW7357_200min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L20_exp230501_A4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L20_exp230501_A4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L20_exp230501_A4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L20_exp230501_A4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L20_exp230501_A4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L20_exp230501_A4_CJW7357_240min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L20_exp230501_A4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L20_exp230501_A4_CJW7357_240min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L21_exp230502_B1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L21_exp230502_B1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L21_exp230502_B1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L21_exp230502_B1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L21_exp230502_B1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L21_exp230502_B1_CJW7357_060min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L21_exp230502_B1_CJW7357_060min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L21_exp230502_B1_CJW7357_060min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L22_exp230502_B2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L22_exp230502_B2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L22_exp230502_B2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L22_exp230502_B2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L22_exp230502_B2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L22_exp230502_B2_CJW7357_120min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L22_exp230502_B2_CJW7357_120min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L22_exp230502_B2_CJW7357_120min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L23_exp230502_B3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L23_exp230502_B3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L23_exp230502_B3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L23_exp230502_B3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L23_exp230502_B3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L23_exp230502_B3_CJW7357_200min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L23_exp230502_B3_CJW7357_200min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L23_exp230502_B3_CJW7357_200min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L24_exp230502_B4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L24_exp230502_B4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L24_exp230502_B4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L24_exp230502_B4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L24_exp230502_B4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L24_exp230502_B4_CJW7357_240min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000 -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-06-18-MS230511L24_exp230502_B4_CJW7357_240min-arrest_DNArep2.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-06-18-MS230511L24_exp230502_B4_CJW7357_240min-arrest_DNArep2.2x36mers.Caulobacter_crescentus_NA1000.nochrM.ERMTOC -bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Caulobacter_crescentus_NA1000.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -excludeReadsMappingToOtherChromosomes