WGCNA on Small RNA-Seq data

Question

[Lalit]

Hello, I am interested to use WGCNA on small RNA seq data. I wondered what should be my input file? Should I use count files or differential expression file as input? If some one has used WGCNA on small RNA-Seq data then please let me know. Best, Lalit

Answer 1

[GouthamAtla]

All your questions are answered here on FAQ page.

https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html

The input file should be a count matrix of normalised counts of genes across samples.

This file should not be filtered for only differentially expressed genes. May be you can remove genes that have very low expression values to reduce the noise in the dataset.

It does not matter what data it is ( whether RNA-Seq or small-RNA ) as long as it is properly normalised.