lncRNA-seq without a reference?

Question

[manekineko]

Hi all,

I have a lncRNA-seq and the species is without a reference genome/transcriptome? Any possible thoughts how i can analyse it? I was hoping i can get some pre-miRNAs info but that was not the case, so i wonder how i can get anything more out of it?

Answer 1

[colindaven]

I assume you have mRNA-seq libraries.

You could use Trinity to create a de novo assembly of the transcriptome.

Then use interpro/blasx/mmseqs/diamond etc to annotate protein coding genes.

Lastly remove those transcripts which have relevant domains or similarity to protein coding genes. But be careful, many lncRNAs will have transposase domains among others.

[manekineko]

Thanks,

Actually I may be interested also in protein coding genes too.

I use Trinity and rnaSpades and im a bit confused, Trinity produce only 10k transcripts, but rnaSpades - 300k……!? (With more or less default options, just with strand specific FR option)