TSS for lncRNAs from GENCODE

Question

[alex]

Hi,

I downloaded the GENCODE annotations for all lncRNAs and noticed that there are often multiple transcripts per gene, with transcripts having different start positions than genes.

If I want all possible TSS for all lncRNAs, should I include both the gene AND transcript start sites?

Does "transcript" refer to the positions of a transcript after it has been processed or is this the entire extent of the transcribed region?

Thanks!

Answer 1

[Charles Plessy]

If it is not too late, have a look at the "FANTOM CAT", which is "an atlas of human long non-coding RNAs with accurate 5′ ends".