Is it possible to detect lncRNA in a de novo assembled genome?
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4.9 years ago
Reza ▴ 10

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,

RNA-Seq Assembly genome • 1.2k views
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Yes, if those transcripts are long enough and do not have any coding potential.

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Thank you for your answer.

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

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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.

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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?

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Hi Wouter,

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

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4.7 years ago

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.

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