cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62/At_BLJ_YFP_1-GSM1463808.36mers.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/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_1-GSM1463808.36mers.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/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_1-GSM1463808.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62/At_BLJ_YFP_2-GSM1463810.36mers.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/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_2-GSM1463810.36mers.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/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_2-GSM1463810.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62/At_JKD_YFP_1-GSM1463812.36mers.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/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_1-GSM1463812.36mers.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/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_1-GSM1463812.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62/At_JKD_YFP_2-GSM1463814.36mers.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/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_2-GSM1463814.36mers.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/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_2-GSM1463814.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62/At_Control-GSM1463816.36mers.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/62-organelles-nucleus-merged-k3m2/At_Control-GSM1463816.36mers.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/62-organelles-nucleus-merged-k3m2/At_Control-GSM1463816.36mers