Some book about clustering algorithms for RNA-Seq data?

Question

[cristian.cornejo]

Hi, i am a student of computer engineering. I am going to make a investigation about a clustering algorithm for RNA-Seq data and incorporating biological annotations... I need a book about this. Mainly about clustering algorithms for RNA-Seq.

Respects from Chile!

[Istvan Albert]

Well there may not be such concept as clustering specifically designed for RNA-seq data. The RNA-Seq results are usually presented in a matrix like row/colum format where the rows are genes and the columns correspond to samples/treatments.

This data is then clustered with traditional clustering methods where both a similarity metric and a linkage needs to be specified.

I suggest to look at a few posts on the right side of this post for an introduction to these concepts.

Here is an overview: A: Clustering Gene Expression For Time Course Rna-Seq Data

Answer 1

[cristian.cornejo]

I made experiments with clustering of microarray data (matrix of expression). There are several approaches and studies about clusterings algorithms for microarray data. Although the microarray and RNA-Seq data results can use the same data structure (matrix of expression) these are different. For example in the sensitivity. Also there are several scientific articles about clustering for this kind of data. For example Model-based clustering for RNA-Seq data (doi:10.1093/bioinformatics/btt632). Therefore there might be a book about it.

[Istvan Albert]

I see it wasn't clear from your original post what level of complexity you are looking for. I would suggest to look at papers rather than search for a book, most books lag technology by some years and RNA-Seq is a quite novel field.