python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 19786_Fis_HS_i5006_DY330_rep1.end1.fastq.gz 19786_Fis_HS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fis_HS_i5006_DY330_rep1_19786.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20238_Fis_HS_i5006_DY330_rep2.end1.fastq.gz 20238_Fis_HS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fis_HS_i5006_DY330_rep2_20238.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 19780_Fis_MHS_i5006_DY330_rep1.end1.fastq.gz 19780_Fis_MHS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fis_MHS_i5006_DY330_rep1_19780.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20234_Fis_MHS_i5006_DY330_rep1.end1.fastq.gz 20234_Fis_MHS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Fis_MHS_i5006_DY330_rep1_20234.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20227_HimD_HS_i5006_DY330_rep1.end1.fastq.gz 20227_HimD_HS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HimD_HS_i5006_DY330_rep1_20227.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20228_HimD_HS_i5006_DY330_rep2.end1.fastq.gz 20228_HimD_HS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HimD_HS_i5006_DY330_rep2_20228.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21327_HimD_HS_i5006_DY330_rep3.end1.fastq.gz 21327_HimD_HS_i5006_DY330_rep3.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HimD_HS_i5006_DY330_rep3_21327.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20219_HimD_MHS_i5006_DY330_rep1.end1.fastq.gz 20219_HimD_MHS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HimD_MHS_i5006_DY330_rep1_20219.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20220_HimD_MHS_i5006_DY330_rep2.end1.fastq.gz 20220_HimD_MHS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HimD_MHS_i5006_DY330_rep2_20220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21320_HimD_MHS_i5006_DY330_rep3.end1.fastq.gz 21320_HimD_MHS_i5006_DY330_rep3.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HimD_MHS_i5006_DY330_rep3_21320.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17259_MglB_HS_i5006_DY330_rep1.end1.fastq.gz 17259_MglB_HS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MglB_HS_i5006_DY330_rep1_17259.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17274_MglB_HS_i5006_DY330_rep2.end1.fastq.gz 17274_MglB_HS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MglB_HS_i5006_DY330_rep2_17274.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17251_MglB_MHS_i5006_DY330_rep1.end1.fastq.gz 17251_MglB_MHS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MglB_MHS_i5006_DY330_rep1_17251.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17267_MglB_MHS_i5006_DY330_rep2.end1.fastq.gz 17267_MglB_MHS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MglB_MHS_i5006_DY330_rep2_17267.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 19790_RpoA_HS_i5006_DY330_rep1.end1.fastq.gz 19790_RpoA_HS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoA_HS_i5006_DY330_rep1_19790.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20240_RpoA_HS_i5006_DY330_rep2.end1.fastq.gz 20240_RpoA_HS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoA_HS_i5006_DY330_rep2_20240.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21307_RpoA_HS_i5006_DY330_rep3.end1.fastq.gz 21307_RpoA_HS_i5006_DY330_rep3.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoA_HS_i5006_DY330_rep3_21307.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 19784_RpoA_MHS_i5006_DY330_rep1.end1.fastq.gz 19784_RpoA_MHS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoA_MHS_i5006_DY330_rep1_19784.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20236_RpoA_MHS_i5006_DY330_rep2.end1.fastq.gz 20236_RpoA_MHS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoA_MHS_i5006_DY330_rep2_20236.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21299_RpoA_MHS_i5006_DY330_rep3.end1.fastq.gz 21299_RpoA_MHS_i5006_DY330_rep3.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoA_MHS_i5006_DY330_rep3_21299.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17260_RpoB_HS_i5006_DY330_rep1.end1.fastq.gz 17260_RpoB_HS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoB_HS_i5006_DY330_rep1_17260.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17275_RpoB_HS_i5006_DY330_rep2.end1.fastq.gz 17275_RpoB_HS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoB_HS_i5006_DY330_rep2_17275.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21322_RpoB_HS_i5006_DY330_rep3.end1.fastq.gz 21322_RpoB_HS_i5006_DY330_rep3.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoB_HS_i5006_DY330_rep3_21322.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17252_RpoB_MHS_i5006_DY330_rep1.end1.fastq.gz 17252_RpoB_MHS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoB_MHS_i5006_DY330_rep1_17252.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17268_RpoB_MHS_i5006_DY330_rep2.end1.fastq.gz 17268_RpoB_MHS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoB_MHS_i5006_DY330_rep2_17268.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21315_RpoB_MHS_i5006_DY330_rep3.end1.fastq.gz 21315_RpoB_MHS_i5006_DY330_rep3.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoB_MHS_i5006_DY330_rep3_21315.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20231_RpoC_HS_i5006_DY330_rep1.end1.fastq.gz 20231_RpoC_HS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoC_HS_i5006_DY330_rep1_20231.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20232_RpoC_HS_i5006_DY330_rep2.end1.fastq.gz 20232_RpoC_HS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoC_HS_i5006_DY330_rep2_20232.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21323_RpoC_HS_i5006_DY330_rep3.end1.fastq.gz 21323_RpoC_HS_i5006_DY330_rep3.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoC_HS_i5006_DY330_rep3_21323.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21324_RpoC_HS_i5006_DY330_rep4.end1.fastq.gz 21324_RpoC_HS_i5006_DY330_rep4.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoC_HS_i5006_DY330_rep4_21324.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20223_RpoC_MHS_i5006_DY330_rep1.end1.fastq.gz 20223_RpoC_MHS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoC_MHS_i5006_DY330_rep1_20223.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20224_RpoC_MHS_i5006_DY330_rep2.end1.fastq.gz 20224_RpoC_MHS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoC_MHS_i5006_DY330_rep2_20224.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21316_RpoC_MHS_i5006_DY330_rep3.end1.fastq.gz 21316_RpoC_MHS_i5006_DY330_rep3.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoC_MHS_i5006_DY330_rep3_21316.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21317_RpoC_MHS_i5006_DY330_rep4.end1.fastq.gz 21317_RpoC_MHS_i5006_DY330_rep4.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoC_MHS_i5006_DY330_rep4_21317.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17261_RpoD_HS_i5006_DY330_rep1.end1.fastq.gz 17261_RpoD_HS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoD_HS_i5006_DY330_rep1_17261.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17276_RpoD_HS_i5006_DY330_rep2.end1.fastq.gz 17276_RpoD_HS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoD_HS_i5006_DY330_rep2_17276.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17253_RpoD_MHS_i5006_DY330_rep1.end1.fastq.gz 17253_RpoD_MHS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoD_MHS_i5006_DY330_rep1_17253.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17269_RpoD_MHS_i5006_DY330_rep2.end1.fastq.gz 17269_RpoD_MHS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoD_MHS_i5006_DY330_rep2_17269.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17265_RpoH_HS_i5006_DY330_rep1.end1.fastq.gz 17265_RpoH_HS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoH_HS_i5006_DY330_rep1_17265.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17280_RpoH_HS_i5006_DY330_rep2.end1.fastq.gz 17280_RpoH_HS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoH_HS_i5006_DY330_rep2_17280.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21313_RpoH_HS_i5006_DY330_rep3.end1.fastq.gz 21313_RpoH_HS_i5006_DY330_rep3.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoH_HS_i5006_DY330_rep3_21313.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21314_RpoH_HS_i5006_DY330_rep4.end1.fastq.gz 21314_RpoH_HS_i5006_DY330_rep4.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoH_HS_i5006_DY330_rep4_21314.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17257_RpoH_MHS_i5006_DY330_rep1.end1.fastq.gz 17257_RpoH_MHS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoH_MHS_i5006_DY330_rep1_17257.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17273_RpoH_MHS_i5006_DY330_rep2.end1.fastq.gz 17273_RpoH_MHS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoH_MHS_i5006_DY330_rep2_17273.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21305_RpoH_MHS_i5006_DY330_rep3.end1.fastq.gz 21305_RpoH_MHS_i5006_DY330_rep3.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoH_MHS_i5006_DY330_rep3_21305.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21306_RpoH_MHS_i5006_DY330_rep4.end1.fastq.gz 21306_RpoH_MHS_i5006_DY330_rep4.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoH_MHS_i5006_DY330_rep4_21306.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20229_RpoN_HS_i5006_DY330_rep1.end1.fastq.gz 20229_RpoN_HS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoN_HS_i5006_DY330_rep1_20229.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20230_RpoN_HS_i5006_DY330_rep2.end1.fastq.gz 20230_RpoN_HS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoN_HS_i5006_DY330_rep2_20230.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20221_RpoN_MHS_i5006_DY330_rep1.end1.fastq.gz 20221_RpoN_MHS_i5006_DY330_rep1.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoN_MHS_i5006_DY330_rep1_20221.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20222_RpoN_MHS_i5006_DY330_rep2.end1.fastq.gz 20222_RpoN_MHS_i5006_DY330_rep2.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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 20 -v 1 -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/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RpoN_MHS_i5006_DY330_rep2_20222.PE.a