[maker-devel] model_gff question

[Carson Holt]

They can be replaced under two circumstances.
1. If you provide two model_gff files (comma separated list), in which case
MAKER thinks it is merging legacy annotations and will only keep one or the
other if models overlap.
2. If you turn snap, augusutus, genemark, or est2genome on.  MAKER sees this
as a cue that if these other programs produce a better model, it can replace
the current model.  If you set map_forward=1, MAKER will conserve the name
of the previous model (so models change structure but names are conserved);
otherwise, it gets a new name.  Sometimes groups like to rename models every
time their is a structural change.  I think you are supposed to get the
Alias attribute set when you don't get names mapped forward though (I can't
remember if I added this or just planned on adding the Alias mapping
though).

MAKER should never drop a model_gff model.  It can only replace it if
something better comes along, but it should not disappear.

Thanks,
Carson


From:  Michael Thon <mike.thon at gmail.com>
Date:  Monday, 1 October, 2012 1:53 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] model_gff question

Under what circumstances will maker not include a gene model from the
model_gff file in its final output?  It was my understanding from this post:
 https://groups.google.com/d/topic/maker-devel/Y5jSdZ1Olcc/discussion

That maker will keep or replace models in model_gff and never remove them.
I'm reannotating a fungal genome and in model_gff I'm providing the gene
models originally made by the sequencing center.  I have 12006 models in the
file I specify in model_gff but maker's final annotation has only 10727
models in it.  
-Mike

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