Is it possible to detect lncRNA in a de novo assembled genome?

Question

[Reza]

Hello everybody,

I have RNAseq data from species that the genome reference is not available and I'd like detect lncRNA. Do you think that this is possible?

Thanks,

[Sishuo Wang]

Yes, if those transcripts are long enough and do not have any coding potential.

[Reza]

Thank you for your answer.

[ATpoint]

Could you elaborate on the preferred strategy and tools to do that.

[Antonio Camargo]

There are some tools that can distinguish between lncRNAs and mRNAs even if the transcript sequence is incomplete (as you would expect in a de novo assembly). You can check Figure 5 here.

[WouterDeCoster]

Your title says that you have a de novo assembled genome, but your question is about a species with (reference) genome, so what is it?

[Reza]

Hi Wouter,

I assembled the raw reads into transcripts (contigs) and used it as reference genome.

Answer 1

[grant.hovhannisyan]

No problem, just assemble the transcripts and then assess their coding potentials. Would be good to use several tools for coding potential and then see if their results overlap.