plant long non-coding RNA

Question

[Sam]

Dear All

could you introduce an appropriate pipeline to the predicate and identify lncRNA according to RNA-seq data in plants?

Thanks

[cschu181]

Just some ideas:

If your data is not ribo-depleted, first filter against an rRNA database, e.g. sortmeRNA.

If you have a reference genome and annotation: map against that, remove all hits against known protein-coding RNA, assemble the remaining reads.

If you don't have a reference genome/annotation, assemble the reads, remove all transcripts with ORFs that yield good matches against protein-coding RNAs, e.g. by blastx against nr.

For identification you could run Infernal on the set of remaining transcripts.

Answer 1

[colindaven]

Here's a couple, but as far as I remember not many are plant specific

https://academic.oup.com/nar/article/45/22/e183/4282667

https://www.lncrnablog.com/uclncr-ultrafast-and-comprehensive-long-non-coding-rna-detection-from-rna-seq-2/