canonical transcript from vep
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Entering edit mode
6 weeks ago

I am using VEP and I wonder which transcript to report. I am aware this is an opinionated question.

Furthermore, I know VEP has a canonical transcript field, but in fact this follow the longest transcript rule as described here: How does VEP decide on canonical transcripts and is there a list?

VEP also give "appris" and "tsl" score.

Because It can often change the result, I wonder I if I can do better than "the longest rule" when possible. Does it exist a state-of-the-art method to pick the "Canonical transcript" (i.e. a supported transcript likely to be the majority one).

ensembl transcript appris canonical tsl • 133 views
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Entering edit mode
6 weeks ago

No, that's been updated since then. Details here.

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