cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776542 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - mvfR1-GSM1593043.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776543 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - mvfR2-GSM1593044.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776544 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - soxR1-GSM1593045.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776545 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - soxR2-GSM1593046.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776546 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - rpoN1-GSM1593047.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776547 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - rpoN2-GSM1593048.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776548 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - vfr1-GSM1593049.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776549 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - vfr2-GSM1593050.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776550 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - algR1-GSM1593051.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776551 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - algR2-GSM1593052.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776552 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - exsA1-GSM1593053.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776553 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - exsA2-GSM1593054.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776554 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - gacA1-GSM1593055.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776555 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - gacA2-GSM1593056.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776556 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - 2588-1-GSM1593057.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776557 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - 2588-2-GSM1593058.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776558 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - mexT1-GSM1593059.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776559 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - mexT2-GSM1593060.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776560 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - wspR1-GSM1593061.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/41-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1776561 | 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/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - wspR2-GSM1593062.36mers.unique