cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58/AtDEK3_OE3-1-GSM1348068.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1-GSM1348068.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1-GSM1348068.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58/AtDEK3_OE3-1_input-GSM1348069.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1_input-GSM1348069.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1_input-GSM1348069.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58/AtDEK3_OE9-1-GSM1348070.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1-GSM1348070.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1-GSM1348070.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58/AtDEK3_OE9-1_inout-GSM1348071.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1_inout-GSM1348071.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1_inout-GSM1348071.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58/AtDEK3_OE17-4-GSM1348072.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4-GSM1348072.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4-GSM1348072.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58/AtDEK3_OE17-4_input-GSM1348073.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4_input-GSM1348073.36mers.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/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4_input-GSM1348073.36mers