[maker-devel] Consensus gene models

[Carson Holt]

The consensus list is in the maker.proteins.fasta and
maker.transcripts.fasta file.  The predictor specific lists are just for
reference purposes (incase you want to see what the other predictors
produced on their own, i.e. without MAKER's intervention).  The
non-overlapping.fasta file in the same directory will contain consensus
entries for models that were not supported by any evidence and don't overlap
any gene models in the  maker.transcripts.fasta (think of these as the maybe
gene and the maker.transcripts.fasta as the very likely genes).  You can set
keep_preds=1 if you just want MAKER to keep everything with or without
support and just produce consensus (probably ok on a fungus, but I wouldn't
recommend it on other eukayotes because false positive rates will be very
high).

Thanks,
Carson



From:  Eduardo Larriba <larriba.ed at gmail.com>
Date:  Friday, 25 May, 2012 12:01 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Consensus gene models

Hi Carson and people,
I am working on structural annotation of a filamentous fungus, of which
there is little evidence as EST or Protein. For generate consensus gene
based on limited evidences to me I used  Marker.
 For this I created the files GeneMark prediction-is and SNAP.
 I run maker using the EST of my organims (85), along with 5700 EST of the
closed organims. I have made ​​predictions with Augustus, and SNAP
GeneMark, with the training files for my organims, in Maker pipeline.
Everything works fine.
 My problem is that when I get the consensus sequences of all my contigs,
fasta_merge script (included in Maker), I get different list for each
predictor, as well as when I try to get the gff of all.
 They could tell me how I can use Maker consensus for a list of genes? Or I
have to do it manually? There is the possibility that Maker evaluates the
accuracy of each prediction and confirm, so just get a list of the different
predictions?

 Thank you very much.


-- 
Eduardo Larriba Tornel
Universidad de Alicante.
Lab. Fitopatología
Dept. Ciencias del Mar y Biología Aplicada
Pabellón 13. 
San Vicente del Raspeig
Tel. 96 590 3400 ext 3280

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