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

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?

Thank You

rna-seq rrbs methyl-seq
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written by Neu • Neu

Thank you. It helped

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written by Neu • Neu

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

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written by Santosh Anand Santosh Anand

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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

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written by Santosh Anand Santosh Anand

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