cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67/WK33-HA_mock_14h_rep1-GSM1618741.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_mock_14h_rep1-GSM1618741.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_mock_14h_rep1-GSM1618741.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67/WK33-HA_mock_14h_rep2-GSM1618742.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_mock_14h_rep2-GSM1618742.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_mock_14h_rep2-GSM1618742.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67/WK33-HA_mock_14h_input_rep1-GSM1618743.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_mock_14h_input_rep1-GSM1618743.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_mock_14h_input_rep1-GSM1618743.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67/WK33-HA_mock_14h_input_rep2-GSM1618744.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_mock_14h_input_rep2-GSM1618744.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_mock_14h_input_rep2-GSM1618744.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67/WK33-HA_Bc_14h_rep1-GSM1618745.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_Bc_14h_rep1-GSM1618745.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_Bc_14h_rep1-GSM1618745.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67/WK33-HA_Bc_14h_rep2-GSM1618746.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_Bc_14h_rep2-GSM1618746.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_Bc_14h_rep2-GSM1618746.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67/WK33-HA_Bc_14h_input_rep1-GSM1618747.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_Bc_14h_input_rep1-GSM1618747.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_Bc_14h_input_rep1-GSM1618747.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67/WK33-HA_Bc_14h_input_rep2-GSM1618748.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_Bc_14h_input_rep2-GSM1618748.36mers.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/67-organelles-nucleus-merged-k3m2/WK33-HA_Bc_14h_input_rep2-GSM1618748.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67/WT_mock_14h_rep2-GSM1618749.36mers.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/67-organelles-nucleus-merged-k3m2/WT_mock_14h_rep2-GSM1618749.36mers.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/67-organelles-nucleus-merged-k3m2/WT_mock_14h_rep2-GSM1618749.36mers
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/67/WT_Bc_14h_rep2-GSM1618750.36mers.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/67-organelles-nucleus-merged-k3m2/WT_Bc_14h_rep2-GSM1618750.36mers.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/67-organelles-nucleus-merged-k3m2/WT_Bc_14h_rep2-GSM1618750.36mers