cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/64-organelles-nucleus-merged-k3m2/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR442100 | 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/64-organelles-nucleus-merged-k3m2/PRR5-ChIP-GSM889585.36mers.k3m2
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/64-organelles-nucleus-merged-k3m2/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR442101 | 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/64-organelles-nucleus-merged-k3m2/input-GSM889586.36mers.k3m2