cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-only/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR2046723 SRR2046724 | 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 - TRB1_Wt-_GFP-Trap-GSM1701078.36mers.k3m2
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-only/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR2046725 SRR2046726 | 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 - TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.k3m2
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-only/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR2046727 | 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 - TRB1_Wt-_anti-TRB1-GSM1701080.36mers.k3m2
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-only/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR2046728 SRR2046729 | 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 - TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.k3m2