cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168593 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - AlgU_chip_sample1-GSM1327699.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168594 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - AlgU_chip_sample2-GSM1327700.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168595 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - AlgU_control_sample1-GSM1327701.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168596 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - AlgU_control_sample2-GSM1327702.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168597 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - FecI2_chip_sample1-GSM1327703.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168598 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - FecI2_chip_sample2-GSM1327704.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168599 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - FecI_chip_sample1-GSM1327705.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168600 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - FecI_chip_sample2-GSM1327706.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168601 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - FliA_chip_sample1-GSM1327707.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168602 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - FliA_chip_sample2-GSM1327708.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168603 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - FpvI_chip_sample1-GSM1327709.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168604 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - FpvI_chip_sample2-GSM1327710.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168605 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - PvdS_chip_sample1-GSM1327711.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168606 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - PvdS_chip_sample2-GSM1327712.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168607 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - PvdS_control_sample1-GSM1327713.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168608 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - PvdS_control_sample2-GSM1327714.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168609 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoD_chip_sample1-GSM1327715.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168610 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoD_chip_sample2-GSM1327716.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168611 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoD_FliA_control_sample1-GSM1327717.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168612 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoD_FliA_control_sample2-GSM1327718.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168613 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoH_chip_sample1-GSM1327719.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168614 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoH_chip_sample2-GSM1327720.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168615 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoH_control_sample1-GSM1327721.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168616 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoH_control_sample2-GSM1327722.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168617 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoN_chip_sample1-GSM1327723.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168618 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoN_chip_sample2-GSM1327724.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168619 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoN_RpoS_control_sample1-GSM1327725.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168620 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoN_RpoS_control_sample2-GSM1327726.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168621 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoS_chip_sample1-GSM1327727.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168622 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - RpoS_chip_sample2-GSM1327728.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168623 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - SigX_chip_sample1-GSM1327729.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168624 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - SigX_chip_sample2-GSM1327730.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168625 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - SigX_control_sample1-GSM1327731.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/31-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1168626 | 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 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_aeruginosa_UCBPP-PA14-ASM1462v1/bowtie-indexes/GCA_000014625.1_ASM1462v1_genomic.fa - | samtools sort - SigX_control_sample2-GSM1327732.36mers.unique