cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61/CCA1_ChIPSeq_LL1-GSM1808449.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_LL1-GSM1808449.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_LL1-GSM1808449.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61/CCA1_ChIPSeq_LL2-GSM1808450.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_LL2-GSM1808450.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_LL2-GSM1808450.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61/CCA1_ChIPSeq_LL3-GSM1808451.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_LL3-GSM1808451.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_LL3-GSM1808451.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61/CCA1_ChIPSeq_LD1-GSM1808452.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_LD1-GSM1808452.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_LD1-GSM1808452.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61/CCA1_ChIPSeq_LD2-GSM1808453.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_LD2-GSM1808453.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_LD2-GSM1808453.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61/CCA1_ChIPSeq_ZT14-GSM1808454.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_ZT14-GSM1808454.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_ZT14-GSM1808454.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/61/CCA1_ChIPSeq_Input-GSM1808455.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_Input-GSM1808455.36mers.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/61-organelles-nucleus-merged-k3m2/CCA1_ChIPSeq_Input-GSM1808455.36mers