/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/53-Oryza_sativa-organelles-only/OSH1_ChIP-seq_1-DRR000602.sra | python /N/dc2/projects/marinovg/code/trimfastq.py - 35 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/bowtie-indexes/chrM+chrP -p 16 -v 2 -k 3 -m 2 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/sequence/Oryza_sativa.MSU6.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/53-Oryza_sativa-organelles-only/OSH1_ChIP-seq_1-DRR000602.36mers.k3m2
/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/53-Oryza_sativa-organelles-only/Control-IgG-DRR000603.sra | python /N/dc2/projects/marinovg/code/trimfastq.py - 35 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/bowtie-indexes/chrM+chrP -p 16 -v 2 -k 3 -m 2 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/sequence/Oryza_sativa.MSU6.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/53-Oryza_sativa-organelles-only/Control-IgG-DRR000603.36mers.k3m2