lncRNA analysis tutorial

Question

[najibveto]

hello, I would like to ask if there is some good tutorial concerning analysis of lncRNA along RNAseq analysis? like practical example. thank you for your help.

[Carlo Yague]

What kind of analysis ? Differential expression ? Transcript annotation ? Something else ?

[najibveto]

I would like to learn how to do differential expression of lncRNA from RNAseq data as well discovery of noverl lncRNA. thank you for your answer.

[smileszh]

I also would like to ask how analy RNAseq data sequence to lncRNA

Answer 1

[Carlo Yague]

Generally speaking, doing differential expression (DE) or transcript discovery on lncRNA is no different than on mRNA. The only difference is that lncRNA are often less expressed than mRNA, so you might not have enough reads to analyse all of them.

For DE analysis, it is important to actually consider all transcripts (ncRNA AND mRNA) in the analysis because of the way normalization works. I recommend this tutorial based on the DESeq2 R package.

For transcript discovery, one of the most popular tool is StringTie that performs transcript assembly from short read sequencing experiments. A tutorial is shipped with their Nature Protocol paper.

[najibveto]

thank you so much.

Answer 2

[grant.hovhannisyan]

You can follow this github page where I reproduce all analysis of our recent paper about lncRNAs in Candida yeasts (depending on the species you study you might need to adjust some paratemeters). It covers everything, from lncRNA prediction from raw RNA-Seq data to evolutionary, structural and dif. expression analysis. Drop me an email if you need help

[najibveto]

thank you so much for your comment and help. sorry for the late reply.