python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep1_input-GSM1517647.36mers.unique.bam 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/N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_input-GSM1517647.36mers.k3m2.bam chrM,chrP  | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/sequence/Zea_mays.AGPv3.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_input-GSM1517647.36mers &
python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep1_FEA4_ChIP-GSM1517648.36mers.unique.bam 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/N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_FEA4_ChIP-GSM1517648.36mers.k3m2.bam chrM,chrP  | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/sequence/Zea_mays.AGPv3.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_FEA4_ChIP-GSM1517648.36mers &
python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep2_input-GSM1517649.36mers.unique.bam 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/N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_input-GSM1517649.36mers.k3m2.bam chrM,chrP  | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/sequence/Zea_mays.AGPv3.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_input-GSM1517649.36mers &
python /N/dc2/projects/marinovg/code/MergeBAMPerChr.py samtools /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays/rep2_FEA4_ChIP-GSM1517650.36mers.unique.bam scaffold_68,scaffold_140,scaffold_427,scaffold_236,scaffold_462,scaffold_47,scaffold_119,scaffold_36,scaffold_382,scaffold_494,scaffold_453,scaffold_77,scaffold_328,scaffold_61,scaffold_275,scaffold_124,scaffold_239,scaffold_221,scaffold_235,scaffold_194,scaffold_375,scaffold_196,scaffold_482,scaffold_407,scaffold_312,scaffold_489,scaffold_454,scaffold_84,scaffold_227,scaffold_165,scaffold_37,scaffold_302,scaffold_458,scaffold_33,scaffold_100,scaffold_187,scaffold_296,scaffold_263,scaffold_274,scaffold_436,scaffold_415,scaffold_160,scaffold_411,scaffold_186,scaffold_38,scaffold_21,scaffold_306,scaffold_30,scaffold_11,scaffold_473,scaffold_486,scaffold_278,scaffold_149,scaffold_164,scaffold_82,scaffold_117,scaffold_298,scaffold_132,scaffold_459,scaffold_118,scaffold_493,scaffold_310,scaffold_10,scaffold_169,scaffold_327,scaffold_403,scaffold_209,scaffold_390,scaffold_326,scaffold_487,scaffold_76,scaffold_338,scaffold_158,scaffold_86,scaffold_259,scaffold_204,scaffold_189,scaffold_362,scaffold_414,scaffold_48,scaffold_40,scaffold_25,scaffold_294,scaffold_395,scaffold_126,scaffold_295,scaffold_255,scaffold_339,scaffold_461,scaffold_476,scaffold_356,scaffold_213,scaffold_90,scaffold_426,scaffold_148,scaffold_191,scaffold_443,scaffold_231,scaffold_1,scaffold_444,scaffold_24,scaffold_156,scaffold_471,scaffold_70,scaffold_265,scaffold_183,scaffold_372,scaffold_420,scaffold_438,scaffold_346,scaffold_488,scaffold_297,scaffold_365,scaffold_341,scaffold_15,scaffold_325,scaffold_218,scaffold_399,scaffold_320,scaffold_28,scaffold_18,scaffold_168,scaffold_32,scaffold_113,scaffold_111,scaffold_343,scaffold_283,scaffold_91,scaffold_29,scaffold_136,scaffold_342,scaffold_307,scaffold_409,scaffold_439,scaffold_45,scaffold_65,scaffold_16,scaffold_305,scaffold_22,scaffold_321,scaffold_271,scaffold_234,scaffold_102,scaffold_421,scaffold_347,scaffold_75,scaffold_178,scaffold_418,scaffold_95,scaffold_9,scaffold_54,scaffold_237,scaffold_173,scaffold_50,scaffold_129,scaffold_155,scaffold_128,scaffold_116,scaffold_122,scaffold_350,scaffold_447,scaffold_279,scaffold_430,scaffold_87,scaffold_330,scaffold_185,scaffold_83,scaffold_103,scaffold_355,scaffold_388,scaffold_120,scaffold_273,scaffold_470,scaffold_361,scaffold_264,scaffold_269,scaffold_205,scaffold_220,scaffold_110,scaffold_370,scaffold_385,scaffold_354,scaffold_190,scaffold_13,scaffold_208,scaffold_62,scaffold_464,scaffold_366,scaffold_251,scaffold_329,scaffold_292,scaffold_410,scaffold_428,scaffold_167,scaffold_51,scaffold_417,scaffold_92,scaffold_195,scaffold_293,scaffold_308,scaffold_468,scaffold_176,scaffold_93,scaffold_8,scaffold_261,scaffold_184,scaffold_474,scaffold_144,scaffold_246,scaffold_81,scaffold_241,scaffold_233,scaffold_398,scaffold_301,scaffold_367,scaffold_80,scaffold_200,scaffold_175,scaffold_478,scaffold_7,scaffold_373,scaffold_331,scaffold_180,scaffold_53,scaffold_313,scaffold_240,scaffold_266,scaffold_425,scaffold_317,scaffold_348,scaffold_369,scaffold_224,scaffold_96,scaffold_104,scaffold_188,scaffold_106,scaffold_56,scaffold_422,scaffold_222,scaffold_172,scaffold_371,scaffold_66,scaffold_380,scaffold_437,scaffold_423,scaffold_455,scaffold_401,scaffold_88,scaffold_449,scaffold_139,scaffold_41,scaffold_247,scaffold_416,scaffold_465,scaffold_193,scaffold_393,scaffold_311,scaffold_202,scaffold_337,scaffold_477,scaffold_197,scaffold_378,scaffold_4,scaffold_446,scaffold_318,scaffold_451,scaffold_349,scaffold_206,scaffold_64,scaffold_402,scaffold_406,scaffold_141,scaffold_485,scaffold_5,scaffold_59,scaffold_228,scaffold_52,scaffold_258,scaffold_60,scaffold_413,scaffold_363,scaffold_123,scaffold_377,scaffold_85,scaffold_67,scaffold_353,scaffold_322,scaffold_244,scaffold_254,scaffold_27,scaffold_424,scaffold_394,scaffold_20,scaffold_14,scaffold_6,scaffold_492,scaffold_290,scaffold_232,scaffold_483,scaffold_257,scaffold_57,scaffold_374,scaffold_386,scaffold_23,scaffold_73,scaffold_285,scaffold_219,scaffold_154,scaffold_400,scaffold_490,scaffold_404,scaffold_174,scaffold_72,scaffold_225,scaffold_358,scaffold_452,scaffold_472,scaffold_138,scaffold_98,scaffold_491,scaffold_479,scaffold_163,scaffold_359,scaffold_215,scaffold_211,scaffold_159,scaffold_392,scaffold_253,scaffold_284,scaffold_314,scaffold_352,scaffold_34,scaffold_182,scaffold_105,scaffold_3,scaffold_131,scaffold_384,scaffold_336,scaffold_161,scaffold_112,scaffold_381,scaffold_216,scaffold_463,scaffold_303,scaffold_262,scaffold_42,scaffold_309,scaffold_357,scaffold_198,scaffold_323,scaffold_248,scaffold_192,scaffold_270,scaffold_412,scaffold_108,scaffold_199,scaffold_484,scaffold_177,scaffold_166,scaffold_450,scaffold_286,scaffold_419,scaffold_58,scaffold_429,scaffold_324,scaffold_125,scaffold_107,scaffold_109,scaffold_207,scaffold_397,scaffold_121,scaffold_287,scaffold_69,scaffold_396,scaffold_201,scaffold_249,scaffold_223,scaffold_457,scaffold_272,scaffold_153,scaffold_115,scaffold_267,scaffold_152,scaffold_304,scaffold_217,scaffold_242,scaffold_127,scaffold_379,scaffold_334,scaffold_448,scaffold_433,sc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/N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_FEA4_ChIP-GSM1517650.36mers.k3m2.bam chrM,chrP  | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/sequence/Zea_mays.AGPv3.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_FEA4_ChIP-GSM1517650.36mers &