I need a help understanding this please I am new to long non coding RNA and my background is computational.
When I run a lncRNA tool to detect a novel lncRNA, it finds a lncRNA x for example. when I look this x up in public data bases it is annotated as protein coding.
Does this mean the tool has a new evidence that makes x a lncRNA not protein coding?
And most tools runs per trancsript. When I annotate the transcripts, we can have a gene found say in 5 transcripts. 2 of those transcripts are predicted as non coding and the rest as coding. can I safely say, this gene is a lncRNA, or all the transcripts that the gene span have to be non coding to say the gene is a lncRNA? The goal is to find differentially expressed lncRNA at some point.