How to make annotation file for WGCNA analysis of RNA Seq data?
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!
• 1,526 views
•
link
updated
by
Kevin Blighe
•
written
by
mathavanbioinfo
•
written
by
mathavanbioinfo
1 answer
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
• 0 views
•
link
written
by
Kevin Blighe
Log in to answer this question.
More posts like this
-
ProbeID to Gene Symbol Mapping in Microarray data analysis using R
written by Manish •
-
RNAseq matrix input for WGCNA analysis
written by cardon.chc •
-
WGCNA package for R - Gene coexpression analysis
written by sofiablancoglez •
-
Find top genes that correlate with my gene of interest using WGCNA
written by StartR •
-
How create annotation file for WGCNA for RNA-Seq data?
written by mathavanbioinfo
-
How to convert agilent probe id into gene symbol in gene expression matrix?
written by mathavanbioinfo
-
Best practices for differential expression analysis
written by flogin
-
WGCNA analysis for bisulfite data.
written by archi •
-
How to get Gene Co-expression Network from RNA seq data using cor() function?
written by aiswaryabioinfo •
-
single probe represent multiple genes?
written by mathavanbioinfo
