[maker-devel] Maker pass-through behavior

[Marc P. Hoeppner]

Dear list,

I have started using Maker to explore its use for a number of genome 
projects we are planning on running. One of the tools we intend on 
incorporating into our pipeline is PASA (Since we will be using Trinity 
etc). The (cleaned) output with predicted gene structures I would like 
to pass to Maker as pass-through annotation (I am optimistic that 
way...) - but I noticed that doing so does not always result in the 
incorporation of the PASA gene model into the final maker annotation 
track. Sometimes it seems to be superseded by an Augustus/Maker model, 
sometimes the region stays empty (even tho a protein alignment is present).

So my question is how Maker handles pass-throughs, exactly. Can it 
reject pass-throughs, or should it always use such models over any other 
data source? Is there any scenario were it wouldn't?

I understand that Maker uses some internal scoring system to estimate 
the accuracy of an annotation - could that be a reason? It would be a 
bit odd tho, since a lift-over from chicken (to our bird genome) seems 
to support gene models produced by PASA, yet they are nowhere to be 
found in the final models.

And a related question: Is there  a comprehensive documentation where I 
can get more information on the internal decision making process of 
Maker? Or do I have to dig into the code for that?

Cheers,

Marc

PS I have attached a screenshot of such an example - the green track is 
Maker with proteins + augustus (chicken models) + PASA pass-through of a 
cleaned-up gene structure file. (Orange: Cleaned ORFs directly from PASA 
output, Grey: PASA ORFs without cleaning, Dark red: Maker with proteins 
and trinity transcripts as EST evidence, Black: chicken lift-overs from 
EnsEMBL)
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