Annotation Related after WGBS Data Analysis
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2.1 years ago

Hello I am working with WGBS Data. I am using MethyKit package.

MethyKit has provided a reference bed file in the extdata folder, which looks like below. My question is how can I find its header?

chr20   33506636    33563217    NM_007186   0   +   33513606    33562869    0   35  350,71,123,289,57,83,166,107,252,97,102,159,179,183,145,147,231,194,128,170,168,135,144,134,139,349,122,121,122,2616,114,156,102,57,612,    0,2902,4580,6867,8177,10345,10641,11568,11906,14492,16652,17275,17976,18472,20104,21051,22473,23833,24248,24578,35240,35815,38033,39128,41183,42325,43201,44655,46449,46995,52344,52641,53549,54604,55969,

chr20   8061295 8813547 NM_015192   0   +   8061298 8810496 0   32  102,78,69,138,80,54,76,101,167,147,158,83,85,178,68,97,85,125,155,165,100,105,110,133,54,220,181,77,90,58,87,3279,  0,17645,238733,495645,513453,515251,516725,524535,525889,552283,564977,576021,583615,585022,589705,592007,594660,596401,600589,604379,606612,607695,608815,624397,627758,632490,641890,655800,655984,656869,657526,748973,

chr20   8061295 8813547 NM_182734   0   +   8061298 8730801 0   33  102,78,69,138,80,54,76,101,167,147,158,83,85,178,68,97,85,125,155,165,100,105,110,133,54,220,181,77,90,58,87,118,3279,  0,17645,238733,495645,513453,515251,516725,524535,525889,552283,564977,576021,583615,585022,589705,592007,594660,596401,600589,604379,606612,607695,608815,624397,627758,632490,641890,655800,655984,656869,657526,669407,748973,

chr20   3138055 3152506 NM_181493   0   +   3138197 3152108 0   8   157,58,65,74,32,116,77,495, 0,3759,3909,4575,5871,9107,12431,13956,

chr20   1041905 1096426 NM_178578   0   +   1047416 1093724 0   8   147,150,153,83,186,54,159,2754, 0,5490,12235,14163,21858,49868,51056,51767,

next-gen sequencing • 334 views
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what are you looking for? Methylkit ext data is example bed data.

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You kind of asked this before: Reference file Annotation

Note that these extdata often example data to demonstrate functions of the package. I would never use them productively unless code and proper documentation is provided how these were created. Do you need CpG coordinates, then follow the advise of Kevin in this other thread.