cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/63-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/63/prr9-1_PRR9_HA-PRR9_CCR2_LUC_109_Input-GSM1833650.36mers.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/63-organelles-nucleus-merged-k3m2/prr9-1_PRR9_HA-PRR9_CCR2_LUC_109_Input-GSM1833650.36mers.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/63-organelles-nucleus-merged-k3m2/prr9-1_PRR9_HA-PRR9_CCR2_LUC_109_Input-GSM1833650.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/63-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/63/prr9-1_PRR9_HA-PRR9_CCR2_LUC_109_Immunoprecipitated-GSM1833651.36mers.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/63-organelles-nucleus-merged-k3m2/prr9-1_PRR9_HA-PRR9_CCR2_LUC_109_Immunoprecipitated-GSM1833651.36mers.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/63-organelles-nucleus-merged-k3m2/prr9-1_PRR9_HA-PRR9_CCR2_LUC_109_Immunoprecipitated-GSM1833651.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/63-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/63/prr9-1_CCR2_LUC_Input-GSM1833652.36mers.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/63-organelles-nucleus-merged-k3m2/prr9-1_CCR2_LUC_Input-GSM1833652.36mers.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/63-organelles-nucleus-merged-k3m2/prr9-1_CCR2_LUC_Input-GSM1833652.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/63-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/63/prr9-1_CCR2_LUC_Immunoprecipitated-GSM1833653.36mers.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/63-organelles-nucleus-merged-k3m2/prr9-1_CCR2_LUC_Immunoprecipitated-GSM1833653.36mers.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/63-organelles-nucleus-merged-k3m2/prr9-1_CCR2_LUC_Immunoprecipitated-GSM1833653.36mers