cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57/pBBM-BBM-YFP-GSM1264686.36mers.unique.bam chrIII-NC_003074,chrII-NC_003071,chrI-NC_003070,chrIV-NC_003075,chrV-NC_003076 /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/pBBM-BBM-YFP-GSM1264686.36mers.k3m2.bam chrM,chloroplast  | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/pBBM-BBM-YFP-GSM1264686.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57/pBBM-NLS-GFP-GSM1264687.36mers.unique.bam chrIII-NC_003074,chrII-NC_003071,chrI-NC_003070,chrIV-NC_003075,chrV-NC_003076 /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/pBBM-NLS-GFP-GSM1264687.36mers.k3m2.bam chrM,chloroplast  | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/pBBM-NLS-GFP-GSM1264687.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57/35S-BBM-GFP-GSM1264688.36mers.unique.bam chrIII-NC_003074,chrII-NC_003071,chrI-NC_003070,chrIV-NC_003075,chrV-NC_003076 /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/35S-BBM-GFP-GSM1264688.36mers.k3m2.bam chrM,chloroplast  | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/35S-BBM-GFP-GSM1264688.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57/35S-BBM-GSM1264689.36mers.unique.bam chrIII-NC_003074,chrII-NC_003071,chrI-NC_003070,chrIV-NC_003075,chrV-NC_003076 /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/35S-BBM-GSM1264689.36mers.k3m2.bam chrM,chloroplast  | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/57-organelles-nucleus-merged-k3m2/35S-BBM-GSM1264689.36mers