cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66/TRB1_Wt-_GFP-Trap-GSM1701078.36mers.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/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_GFP-Trap-GSM1701078.36mers.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/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_GFP-Trap-GSM1701078.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66/TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.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/66-organelles-nucleus-merged-k3m2/TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.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/66-organelles-nucleus-merged-k3m2/TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66/TRB1_Wt-_anti-TRB1-GSM1701080.36mers.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/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_anti-TRB1-GSM1701080.36mers.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/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_anti-TRB1-GSM1701080.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66/TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.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/66-organelles-nucleus-merged-k3m2/TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.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/66-organelles-nucleus-merged-k3m2/TRB1_TRB1+_anti-TRB1-GSM1701081.36mers