I have som few questions related to the annotation of non-coding transcripts. Hopefully, someone here knows some or all the answers.
Does someone know what does it mean the Transcript support level: NA in some of the transcripts in the Gencode/Ensembl annotation gtf? In their web site, they specified that those transcripts were not analyzed for several reasons transcript quality tags. Then, those non-coding transcripts ou pseudogenes might be suspect and not valid. But, how those transcripts were annotated in their very beginning? What does it mean that they weren't analyzed? How these non-coding transcripts are included in the annotation files? I found that some of them are predicted by algorithms, those algorithms are based on transcripts assemblies alignments or...? and when it says the transcript is 'manually' annotated, what manually is?
I thank in advance the answers.