Question: WGCNA on Small RNA-Seq data
0
gravatar for Lalit
3.9 years ago by
Lalit20
Jodhpur
Lalit20 wrote:

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

ADD COMMENTlink modified 3.9 years ago by geek_y11k • written 3.9 years ago by Lalit20
2
gravatar for geek_y
3.9 years ago by
geek_y11k
Barcelona
geek_y11k wrote:

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 COMMENTlink modified 3.9 years ago • written 3.9 years ago by geek_y11k
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