/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/49-organelles-nucleus-merged-k3m2/YFP-GSM1282365.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/TAIR10/bowtie-indexes/chrM+chloroplast -p 16 -v 2 -k 3 -m 2 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/49-organelles-nucleus-merged-k3m2/YFP-GSM1282365.36mers.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/49-organelles-nucleus-merged-k3m2/pHBI1-HBI1-YFP-GSM1282366.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/TAIR10/bowtie-indexes/chrM+chloroplast -p 16 -v 2 -k 3 -m 2 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/49-organelles-nucleus-merged-k3m2/pHBI1-HBI1-YFP-GSM1282366.36mers.k3m2