cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353972 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupA-delhuB-mid-exponential_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353974 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupA-delhuB-late-exponential_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353971 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupB_stationary_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353975 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupA-delhuB-transition-to-stationary_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353976 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupA-delhuB-stationary_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353970 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupB_transition-two-stationary_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR357356 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupB-delhuA-mid-exponential_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353978 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupB-delhuA-late-exponential_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353968 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupB_late-exponential_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353979 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupB-delhuA-transition-to-stationary_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353980 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupB-delhuA-stationary_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353967 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupB_mid-exponential_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353966 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupA_stationary_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353964 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupA_transition-to-stationary_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353963 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupA_late-exponential_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353962 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - HupA_mid-exponential_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353960 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - IhfB_stationary_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353959 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - IhfB_transition-to-stationary_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353958 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - IhfB_late-exponential_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353957 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - IhfB_mid-exponential_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353933 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - IhfD_stationary_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353932 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - IhfA_transition-to-stationary.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353931 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - IhfA_late-exponential_phase.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/19-Escherichia_coli_str._K-12; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR353930 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Escherichia_coli_str._K-12_substr._MG1655-ASM584v2/bowtie-indexes/GCA_000005845.2_ASM584v2_genomic.fa - | samtools sort - IhfA_mid-exponential_phase.36mers.unique