lncRNA Prediction tool

Question

[georgians]

Hello, I have a RNAseq data, I want to predict lncRNA from this data. Please help me in this regard which tool should I use.

Thanks!!

Best

[Tm]

Are you sure, that your data contains lncRNAs? Which kit you have used for library preparation? Because if it enriches polyA then in that case you cannot expect lncRNA in your sample.

Can you also reveal on which organism you are working?

[lieven.sterck]

Not sure if there exists any specific tool for this.

in a nutshell: what people usually do is to align all reads to a genome, filter out those that match protein-coding and the long ones that do not are the lncRNAs . Alternatively you can assemble all your reads, predict ORFs on them and those that are 'long' and does not seem to have a valid ORF are likely the lncRNAs

Answer 1

[Tm]

you are working on human genome then can try using lncFunTK or UClncR. Alternatively you can explore previous biostar post and this article where they have identified lncRNA from wheat transcriprome.