python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py RpoB_glc1_ChIPexo.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 - RpoB_glc1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py RpoB_glc1_ChIPexo.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 - RpoB_glc1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py RpoB_glc2_ChIPexo.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 - RpoB_glc2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py RpoB_glc2_ChIPexo.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 - RpoB_glc2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YafC_glc1_ChIPexo.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 - YafC_glc1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YafC_glc1_ChIPexo.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 - YafC_glc1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YafC_glc2_ChIPexo.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 - YafC_glc2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YafC_glc2_ChIPexo.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 - YafC_glc2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YbaO_glc1_ChIPexo.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 - YbaO_glc1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YbaO_glc1_ChIPexo.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 - YbaO_glc1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YbaO_glc2_ChIPexo.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 - YbaO_glc2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YbaO_glc2_ChIPexo.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 - YbaO_glc2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YbaQ_glc1_ChIPexo.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 - YbaQ_glc1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YbaQ_glc1_ChIPexo.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 - YbaQ_glc1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YbaQ_glc2_ChIPexo.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 - YbaQ_glc2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YbaQ_glc2_ChIPexo.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 - YbaQ_glc2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YbiH_glc1_ChIPexo.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 - YbiH_glc1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YbiH_glc1_ChIPexo.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 - YbiH_glc1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Ybih_glc2_ChIPexo.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 - Ybih_glc2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Ybih_glc2_ChIPexo.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 - Ybih_glc2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ace1_ChIPexp.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 - YdcI_ace1_ChIPexp.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ace1_ChIPexp.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 - YdcI_ace1_ChIPexp.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ace2_ChIPexo.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 - YdcI_ace2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ace2_ChIPexo.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 - YdcI_ace2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_glc1_ChIPexo.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 - YdcI_glc1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_glc1_ChIPexo.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 - YdcI_glc1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_glc2_ChIPexo.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 - YdcI_glc2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_glc2_ChIPexo.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 - YdcI_glc2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ph5_1_ChIPexo.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 - YdcI_ph5_1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ph5_1_ChIPexo.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 - YdcI_ph5_1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ph5_2_ChIPexo.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 - YdcI_ph5_2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ph5_2_ChIPexo.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 - YdcI_ph5_2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ph8_1_ChIPexo.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 - YdcI_ph8_1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ph8_1_ChIPexo.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 - YdcI_ph8_1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ph8_2_ChIPexo.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 - YdcI_ph8_2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YdcI_ph8_2_ChIPexo.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 - YdcI_ph8_2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YddM_glc1_ChIPexo.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 - YddM_glc1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YddM_glc1_ChIPexo.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 - YddM_glc1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YddM_glc2_ChIPexo.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 - YddM_glc2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YddM_glc2_ChIPexo.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 - YddM_glc2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YeiE_glc1_ChIPexo.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 - YeiE_glc1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YeiE_glc1_ChIPexo.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 - YeiE_glc1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YeiE_glc2_ChIPexo.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 - YeiE_glc2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YeiE_glc2_ChIPexo.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 - YeiE_glc2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YheO_glc1_ChIPexo.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 - YheO_glc1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YheO_glc1_ChIPexo.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 - YheO_glc1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YheO_glc2_ChIPexo.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 - YheO_glc2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YheO_glc2_ChIPexo.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 - YheO_glc2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YiaJ_glc1_ChIPexo.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 - YiaJ_glc1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YiaJ_glc1_ChIPexo.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 - YiaJ_glc1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YiaJ_glc2_ChIPexo.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 - YiaJ_glc2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YiaJ_glc2_ChIPexo.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 - YiaJ_glc2_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YieP_glc1_ChIPexo.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 - YieP_glc1_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YieP_glc1_ChIPexo.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 - YieP_glc1_ChIPexo.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YieP_glc2_ChIPexo.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 - YieP_glc2_ChIPexo.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py YieP_glc2_ChIPexo.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 - YieP_glc2_ChIPexo.SE.a