python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.1x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.end1.fastq.gz 2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA01_exp230501_A1_CJW7357_060min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.1x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.end1.fastq.gz 2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA02_exp230501_A2_CJW7357_120min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.1x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.end1.fastq.gz 2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA03_exp230501_A3_CJW7357_200min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.1x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.end1.fastq.gz 2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA04_exp230501_A4_CJW7357_240min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.1x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.end1.fastq.gz 2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA05_exp230502_B1_CJW7357_060min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.1x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.end1.fastq.gz 2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA06_exp230502_B2_CJW7357_120min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.1x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.end1.fastq.gz 2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA07_exp230502_B3_CJW7357_200min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.1x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.end1.fastq.gz 2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2023-09-13-RNA08_exp230502_B4_CJW7357_240min-arrest_total-RNA.2x36mers.Escherichia_coli_str._K-12_substr._MG1655+Caulobacter_crescentus_NA1000.a