python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa/29CHIP_Input-GSM1035301.36mers.unique.bam chrSy,chrUn,chr9,chr10,chr12,chr8,chr11,chr7,chr5,chr6,chr4,chr2,chr3,chr1 /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_Input-GSM1035301.36mers.k3m2.bam chrM,chrP  | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/sequence/Oryza_sativa.MSU6.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_Input-GSM1035301.36mers &
python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa/29CHIP_mock-GSM1035302.36mers.unique.bam chrSy,chrUn,chr9,chr10,chr12,chr8,chr11,chr7,chr5,chr6,chr4,chr2,chr3,chr1 /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_mock-GSM1035302.36mers.k3m2.bam chrM,chrP  | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/sequence/Oryza_sativa.MSU6.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_mock-GSM1035302.36mers &
python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa/MADS29-CHIP_IPsample-GSM1035300.36mers.unique.bam chrSy,chrUn,chr9,chr10,chr12,chr8,chr11,chr7,chr5,chr6,chr4,chr2,chr3,chr1 /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/MADS29-CHIP_IPsample-GSM1035300.36mers.k3m2.bam chrM,chrP  | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/sequence/Oryza_sativa.MSU6.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/MADS29-CHIP_IPsample-GSM1035300.36mers &