cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55/35S-SUC2-Input-rep1-GSM1419602.36mers.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/55-organelles-nucleus-merged-k3m2/35S-SUC2-Input-rep1-GSM1419602.36mers.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/55-organelles-nucleus-merged-k3m2/35S-SUC2-Input-rep1-GSM1419602.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55/35S-SUC2-Input-rep2-GSM1419603.36mers.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/55-organelles-nucleus-merged-k3m2/35S-SUC2-Input-rep2-GSM1419603.36mers.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/55-organelles-nucleus-merged-k3m2/35S-SUC2-Input-rep2-GSM1419603.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55/35S-SUC2-Myc-ChIP-rep1-GSM1419604.36mers.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/55-organelles-nucleus-merged-k3m2/35S-SUC2-Myc-ChIP-rep1-GSM1419604.36mers.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/55-organelles-nucleus-merged-k3m2/35S-SUC2-Myc-ChIP-rep1-GSM1419604.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55/35S-SUC2-Myc-ChIP-rep2-GSM1419605.36mers.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/55-organelles-nucleus-merged-k3m2/35S-SUC2-Myc-ChIP-rep2-GSM1419605.36mers.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/55-organelles-nucleus-merged-k3m2/35S-SUC2-Myc-ChIP-rep2-GSM1419605.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55/MBD7-5-Input-rep1-GSM1419606.36mers.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/55-organelles-nucleus-merged-k3m2/MBD7-5-Input-rep1-GSM1419606.36mers.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/55-organelles-nucleus-merged-k3m2/MBD7-5-Input-rep1-GSM1419606.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55/MBD7-5-Input-rep2-GSM1419607.36mers.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/55-organelles-nucleus-merged-k3m2/MBD7-5-Input-rep2-GSM1419607.36mers.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/55-organelles-nucleus-merged-k3m2/MBD7-5-Input-rep2-GSM1419607.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55/MBD7-5-Myc-ChIP-rep1-GSM1419608.36mers.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/55-organelles-nucleus-merged-k3m2/MBD7-5-Myc-ChIP-rep1-GSM1419608.36mers.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/55-organelles-nucleus-merged-k3m2/MBD7-5-Myc-ChIP-rep1-GSM1419608.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/55/MBD7-5-Myc-ChIP-rep2-GSM1419609.36mers.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/55-organelles-nucleus-merged-k3m2/MBD7-5-Myc-ChIP-rep2-GSM1419609.36mers.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/55-organelles-nucleus-merged-k3m2/MBD7-5-Myc-ChIP-rep2-GSM1419609.36mers