python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Dps_1.fastq.gz 31 -stdout | /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 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/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 - Dps_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Dps_1.fastq.gz 31 -stdout | /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 --sam - | /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 - Dps_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Dps_2.fastq.gz 31 -stdout | /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 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/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 - Dps_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Dps_2.fastq.gz 31 -stdout | /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 --sam - | /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 - Dps_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Fis_1.fastq.gz 31 -stdout | /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 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/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_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Fis_1.fastq.gz 31 -stdout | /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 --sam - | /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_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Fis_2.fastq.gz 31 -stdout | /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 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/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_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Fis_2.fastq.gz 31 -stdout | /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 --sam - | /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_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GyrA_1.fastq.gz 31 -stdout | /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 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/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 - GyrA_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GyrA_1.fastq.gz 31 -stdout | /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 --sam - | /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 - GyrA_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GyrA_2.fastq.gz 31 -stdout | /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 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/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 - GyrA_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GyrA_2.fastq.gz 31 -stdout | /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 --sam - | /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 - GyrA_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GyrB_1.fastq.gz 31 -stdout | /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 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/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 - GyrB_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GyrB_1.fastq.gz 31 -stdout | /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 --sam - | /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 - GyrB_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GyrB_2.fastq.gz 31 -stdout | /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 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/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 - GyrB_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GyrB_2.fastq.gz 31 -stdout | /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 --sam - | /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 - GyrB_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py H-NS_1.fastq.gz 31 -stdout | /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 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/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 - H-NS_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py H-NS_1.fastq.gz 31 -stdout | /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 --sam - | /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 - H-NS_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py H-NS_2.fastq.gz 31 -stdout | /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 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/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 - H-NS_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py H-NS_2.fastq.gz 31 -stdout | /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 --sam - | /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 - H-NS_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HupA_1.fastq.gz 31 -stdout | /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 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/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 - HupA_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HupA_1.fastq.gz 31 -stdout | /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 --sam - | /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 - HupA_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HupA_2.fastq.gz 31 -stdout | /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 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/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 - HupA_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HupA_2.fastq.gz 31 -stdout | /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 --sam - | /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 - HupA_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HupB_1.fastq.gz 31 -stdout | /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 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/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 - HupB_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HupB_1.fastq.gz 31 -stdout | /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 --sam - | /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 - HupB_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HupB_2.fastq.gz 31 -stdout | /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 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/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 - HupB_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HupB_2.fastq.gz 31 -stdout | /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 --sam - | /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 - HupB_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py InfA_1.fastq.gz 31 -stdout | /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 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/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 - InfA_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py InfA_1.fastq.gz 31 -stdout | /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 --sam - | /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 - InfA_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py InfA_2.fastq.gz 31 -stdout | /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 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/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 - InfA_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py InfA_2.fastq.gz 31 -stdout | /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 --sam - | /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 - InfA_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MukB_1.fastq.gz 31 -stdout | /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 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/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 - MukB_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MukB_1.fastq.gz 31 -stdout | /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 --sam - | /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 - MukB_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MukB_2.fastq.gz 31 -stdout | /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 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/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 - MukB_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MukB_2.fastq.gz 31 -stdout | /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 --sam - | /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 - MukB_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py RdgC_1.fastq.gz 31 -stdout | /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 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/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 - RdgC_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py RdgC_1.fastq.gz 31 -stdout | /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 --sam - | /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 - RdgC_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py RdgC_2.fastq.gz 31 -stdout | /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 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/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 - RdgC_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py RdgC_2.fastq.gz 31 -stdout | /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 --sam - | /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 - RdgC_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Rob_1.fastq.gz 31 -stdout | /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 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/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 - Rob_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Rob_1.fastq.gz 31 -stdout | /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 --sam - | /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 - Rob_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Rob_2.fastq.gz 31 -stdout | /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 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/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 - Rob_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Rob_2.fastq.gz 31 -stdout | /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 --sam - | /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 - Rob_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py StpA_1.fastq.gz 31 -stdout | /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 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/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 - StpA_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py StpA_1.fastq.gz 31 -stdout | /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 --sam - | /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 - StpA_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py StpA_2.fastq.gz 31 -stdout | /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 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/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 - StpA_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py StpA_2.fastq.gz 31 -stdout | /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 --sam - | /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 - StpA_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TopA_1.fastq.gz 31 -stdout | /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 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/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 - TopA_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TopA_1.fastq.gz 31 -stdout | /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 --sam - | /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 - TopA_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TopA_2.fastq.gz 31 -stdout | /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 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/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 - TopA_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py TopA_2.fastq.gz 31 -stdout | /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 --sam - | /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 - TopA_2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Tus_1.fastq.gz 31 -stdout | /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 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/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 - Tus_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Tus_1.fastq.gz 31 -stdout | /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 --sam - | /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 - Tus_1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Tus_2.fastq.gz 31 -stdout | /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 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/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 - Tus_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Tus_2.fastq.gz 31 -stdout | /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 --sam - | /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 - Tus_2.SE.a