I am working on a small paper to characterize lncrna in in vitro differentiated neural cells. I started with using gencode annotation file for quantifying lncRNA. Now I came across with several papers suggesting how to find novel lncRNA (lincScore). But then I realized that I am interested in working with annotated lncRNA particularly antisense and lincRNAs. If I find novel lncRNA how can annotate them for being endogenous? Is there an algorithm for mouse? Plus if I just stick with gencode how comprehensive is that annotation (I am using vM17 version)? How often it is used in the field?
P.S.: Sorry for a naive question. Just trying to build my concepts in lncRNA and Bioinformatics. Thanks for sugegstions!