Annotation of ncRNAs from RNA-Seq data

[Husarin]

Dear all,

I'm working with RNA-Seq data and I would like to annotate the small and long non-coding RNAs present in my samples (in two separate steps or even better with a single program).
Can you recommend any programs for that purpose?

For now I considered aligning my reads to a reference genome. But if there were any comprehensive ncRNA databases one could align RNA-Seq reads to, that would be amazing.

All the best!

[allerzbulintini]

Just to clarify, you want to annotate the known non-coding RNAs present in your RNAseq samples? You aren't looking for new ones correct?

If you are working with a well annotated organism, you could align your reads to the reference genome and then use the BiomaRt biotype annotations to pull out genes that are labelled as non-coding RNAs (although you should look through the other biotype tags because often they are broken up into things like ncRNAs, tRNAs, rRNAs, lincRNAs, etc).

I usually work with ensembl annotations so I know for sure that biomart has the biotypes for those. But I think you can also work it so that you get the biotypes for other annotations as well (like refseq or entrez).