cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/39-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1703162 | 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 - PhoB_chip-GSM1563545.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/39-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1703163 | 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 - PhoB_control-GSM1563546.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/39-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1703164 | 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 - PhoB_deletion_mutant_sample1-GSM1563547.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/39-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1703165 | 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 - PhoB_deletion_mutant_sample2-GSM1563548.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/39-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1703166 | 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 - TctD_transposon_mutant_sample1-GSM1563549.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/39-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1703167 | 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 - TctD_transposon_mutant_sample2-GSM1563550.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/39-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1703168 | 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 - PA14_wildtype_sample1-GSM1563551.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/39-Pseudomonas_aeruginosa_UCBPP-PA14; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1703169 | 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 - PA14_wildtype_sample2-GSM1563552.36mers.unique