cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/55-Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR2549976 | 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/Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065/bowtie-indexes/NC_005823+NC_005824 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065/bowtie-indexes/NC_005823+NC_005824.fa - | samtools sort - 40min_total-GSM1900971.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/55-Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR2549977 | 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/Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065/bowtie-indexes/NC_005823+NC_005824 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065/bowtie-indexes/NC_005823+NC_005824.fa - | samtools sort - 40min_LexA-IP-GSM1900972.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/55-Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR2549978 | 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/Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065/bowtie-indexes/NC_005823+NC_005824 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065/bowtie-indexes/NC_005823+NC_005824.fa - | samtools sort - 60min_total-GSM1900973.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/55-Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR2549979 | 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/Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065/bowtie-indexes/NC_005823+NC_005824 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Leptospira_interrogans_serovar_Copenhageni_Fiocruz_L1_130_uid58065/bowtie-indexes/NC_005823+NC_005824.fa - | samtools sort - 60min_LexA-IP-GSM1900974.36mers.unique