cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-only/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1029950 | 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 - pBBM-BBM-YFP-GSM1264686.36mers.k3m2
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-only/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1029951 | 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 - pBBM-NLS-GFP-GSM1264687.36mers.k3m2
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-only/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1029952 | 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 - 35S-BBM-GFP-GSM1264688.36mers.k3m2
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-only/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1029953 | 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 - 35S-BBM-GSM1264689.36mers.k3m2