cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59/RGA_ChIP1-GSM1429897.36mers.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/59-organelles-nucleus-merged-k3m2/RGA_ChIP1-GSM1429897.36mers.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/59-organelles-nucleus-merged-k3m2/RGA_ChIP1-GSM1429897.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59/RGA_ChIP2-GSM1429898.36mers.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/59-organelles-nucleus-merged-k3m2/RGA_ChIP2-GSM1429898.36mers.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/59-organelles-nucleus-merged-k3m2/RGA_ChIP2-GSM1429898.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59/RGA_ChIP3-GSM1429899.36mers.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/59-organelles-nucleus-merged-k3m2/RGA_ChIP3-GSM1429899.36mers.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/59-organelles-nucleus-merged-k3m2/RGA_ChIP3-GSM1429899.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59/WT_ChIP1-GSM1429900.36mers.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/59-organelles-nucleus-merged-k3m2/WT_ChIP1-GSM1429900.36mers.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/59-organelles-nucleus-merged-k3m2/WT_ChIP1-GSM1429900.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59/WT_ChIP2-GSM1429901.36mers.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/59-organelles-nucleus-merged-k3m2/WT_ChIP2-GSM1429901.36mers.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/59-organelles-nucleus-merged-k3m2/WT_ChIP2-GSM1429901.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/59/WT_ChIP3-GSM1429902.36mers.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/59-organelles-nucleus-merged-k3m2/WT_ChIP3-GSM1429902.36mers.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/59-organelles-nucleus-merged-k3m2/WT_ChIP3-GSM1429902.36mers