How to computationally decide sense, antisense, intronic, or intergenic?

[thejustpark]

Hello guys,

I am working on characterizing a specific subset of lncRNAs.
As a way, I am interested in labeling them as sense, antisense, intronic, or intergenic.
I know I can implement a tool for this, but I would be surprised if there are no computational tools out there that do the job.
Then, it would be redundant if I implement this myself.
Do you know of any tool doing this?

Also, have you guys seen any papers talking about their biological roles?
I have googled it, but couldn't find one.
I think it's an interesting topic, so I cannot believe that there is no paper about this.

Thanks,

[swbarnes2]

BEDTools might do it for you. You would compare a .bed file of gene or exon coordinates to your hits, and see what intersects, in what orientation.

[syfo]

Yes, BEDtools or alike. Note that lncRNAs can easily overlap different regions (exon-intron, gene-intergenic, etc), so you'll have to come out with some rule.
As for their function here is a review you might find interesting.

[thejustpark]

Thanks a lot guys.
I will look into BEDTools for this.
Yes, I have to come up with some rule.