cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813200 | 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 - HA69770_HA1-GSM1616430.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813201 | 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 - HA69770_HA2-GSM1616431.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813202 | 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 - HA69770_HA3-GSM1616432.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813203 | 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 - HA69770_empty1-GSM1616433.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813204 | 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 - HA69770_empty2-GSM1616434.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813205 | 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 - HA69770_empty3-GSM1616435.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813206 | 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 - rpoA_HA1-GSM1616436.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813207 | 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 - rpoA_HA2-GSM1616437.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813208 | 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 - rpoA_HA3-GSM1616438.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813209 | 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 - rpoA_empty1-GSM1616439.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813210 | 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 - rpoA_empty2-GSM1616440.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/56-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1813211 | 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 - rpoA_empty3-GSM1616441.36mers.unique