/N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep1_input-GSM1517647.sra | 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/Land_plants/Zea_mays.AGPv3/bowtie-indexes/Zea_mays.AGPv3 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/sequence/Zea_mays.AGPv3.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep1_input-GSM1517647.36mers.unique
/N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep1_FEA4_ChIP-GSM1517648.sra | 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/Land_plants/Zea_mays.AGPv3/bowtie-indexes/Zea_mays.AGPv3 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/sequence/Zea_mays.AGPv3.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep1_FEA4_ChIP-GSM1517648.36mers.unique
/N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep2_input-GSM1517649.sra | 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/Land_plants/Zea_mays.AGPv3/bowtie-indexes/Zea_mays.AGPv3 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/sequence/Zea_mays.AGPv3.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep2_input-GSM1517649.36mers.unique
/N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep2_FEA4_ChIP-GSM1517650.sra | 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/Land_plants/Zea_mays.AGPv3/bowtie-indexes/Zea_mays.AGPv3 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/sequence/Zea_mays.AGPv3.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep2_FEA4_ChIP-GSM1517650.36mers.unique