Question

Integrative analysis of RNA-seq and DNA-methylation study refering different annotation files

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7.8 years ago

Neu ▴ 10

Hi, I have analyzed RNA-seq data where I used GENCODE v 25 annotation. I want to integrate this data with DNA -methylation study that refers hg19 build for alignment. Will it cause any problem?

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RNA-Seq RRBS Methyl-Seq • 1.6k views

ADD COMMENT • link 7.8 years ago by Neu ▴ 10

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Thank you. It helped

ADD REPLY • link 7.8 years ago by Neu ▴ 10

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You should close this thread by accepting the Answer if your Q is answered.

ADD REPLY • link 7.8 years ago by Santosh Anand 5.8k

score 1 · Answer 1 · 2017-03-27

For sure, it will create problem due to different co-ordinate system. Your option is to do liftOver of one genome version to other. Another option is that you re-analyze the RNA-seq with gencode version of hg19 / GRCh37 https://www.gencodegenes.org/releases/25lift37.html

EDIT: On rethinking, It seems to me that if you are interested in just comparing the gene-names, it might not be a problem, also because gencode 25 for hg19 is just a liftOver of coordinates. But for any co-ordinate related thing, it will create trouble. IMO, it is better to have uniform coordinate system wherever possible