How to get information about antisense/sense lncRNAs?

Question

[newbie]

I have around 200 lncRNAs among which 80 are antisense, 50 lincRNAs and 70 are sense overlapping. From Gencode gtf I got to know these gene_type information of lncRNAs.

I am able to know only the genetypes of lncRNAs. But I would like to know more about the antisense and sense lncRNAs. As we know that antisense lncRNAs are antisense to protein coding genes and sense lncRNAs are Long non-coding transcript that contains a coding gene in its intron on the same strand.

I would like to know what are the protein-coding genes these lncRNAs are overlapping with? From where I could get this information? Are there any databases to get this information?

thanq.

Answer 1

[jared.andrews07]

I would like to know what are the protein-coding genes these lncRNAs are overlapping with? From where I could get this information? Are there any databases to get this information?

A bedtools intersect call with your lncRNAs and annotated GTF filtered for protein-coding genes would get you this. Most antisense transcripts are named after the gene they are anti-sense to as well.