WGCNA on Small RNA-Seq data
1
0
Entering edit mode
5.7 years ago
Lalit ▴ 20

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

Small RNA-Seq Gene expression Network Analysis • 1.8k views
ADD COMMENT
2
Entering edit mode
5.7 years ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1278 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6