cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/51-Pseudomonas_savastanoi_pv._phaseolicola; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1410076 | 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_savastanoi_pv._phaseolicola-1448A-ASM1220v1/bowtie-indexes/GCA_000012205.1_ASM1220v1_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_savastanoi_pv._phaseolicola-1448A-ASM1220v1/bowtie-indexes/GCA_000012205.1_ASM1220v1_genomic.fa - | samtools sort - CK-1-GSM1413010.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/51-Pseudomonas_savastanoi_pv._phaseolicola; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1410077 | 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_savastanoi_pv._phaseolicola-1448A-ASM1220v1/bowtie-indexes/GCA_000012205.1_ASM1220v1_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_savastanoi_pv._phaseolicola-1448A-ASM1220v1/bowtie-indexes/GCA_000012205.1_ASM1220v1_genomic.fa - | samtools sort - CK-2-GSM1413011.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/51-Pseudomonas_savastanoi_pv._phaseolicola; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1410078 | 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_savastanoi_pv._phaseolicola-1448A-ASM1220v1/bowtie-indexes/GCA_000012205.1_ASM1220v1_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_savastanoi_pv._phaseolicola-1448A-ASM1220v1/bowtie-indexes/GCA_000012205.1_ASM1220v1_genomic.fa - | samtools sort - RhpR-HA-1-GSM1413012.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/51-Pseudomonas_savastanoi_pv._phaseolicola; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1410079 | 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_savastanoi_pv._phaseolicola-1448A-ASM1220v1/bowtie-indexes/GCA_000012205.1_ASM1220v1_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_savastanoi_pv._phaseolicola-1448A-ASM1220v1/bowtie-indexes/GCA_000012205.1_ASM1220v1_genomic.fa - | samtools sort - RhpR-HA-2-GSM1413013.36mers.unique