python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.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 2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.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 2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.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 2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.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 2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.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 2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.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 2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.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 2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.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 2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.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 2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.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 2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.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 2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.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 2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.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 2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.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 2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.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 2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.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 2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.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 2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.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 2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.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 2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.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 2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.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 2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.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 2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.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 2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.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 2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.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 2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.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 2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.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 2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.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 2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.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 2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.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 2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.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 2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a.bam SAMstats-2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.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