Question: How to make annotation file for WGCNA analysis of RNA Seq data?
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gravatar for mathavanbioinfo
4 months ago by
India
mathavanbioinfo50 wrote:

hello all, I want to study the co-expression analysis using RNA seq data by WGCNA analysis ( Organism- Homosapiens). I created the gene count matrix file (Package - Subread ) as the input file. For mapping the Ensemble ID into the gene symbol, I need a gene annotation file. Please share your knowledge, how to get the gene annotation file!

next-gen • 171 views
ADD COMMENTlink modified 4 months ago by Kevin Blighe63k • written 4 months ago by mathavanbioinfo50
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gravatar for Kevin Blighe
4 months ago by
Kevin Blighe63k
Kevin Blighe63k wrote:

You can just use one of the GENCODE GTFs: https://www.gencodegenes.org/human/

I would use the 'Basic gene annotation CHR'.

Be sure that you are matching based on reference genome version, too. The page to which i linked, by default, as of today (April 9, 2020) is for GRCh38 / hg38.

Kevin

ADD COMMENTlink modified 4 months ago • written 4 months ago by Kevin Blighe63k
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