[maker-devel] Unexpected results with correct_est_fusion

[Carson Holt]

The correct_est_fusion option just clips UTR on overlapping genes.   I
suspect the real problem is setting pred_flank too low.  If your lead in
sequence to a gene is too short, ab initio predictors won't call it.  So you
are probably getting empty reports from SNAP/Augustus for the hint based
predictions.  Try increasing pred_flank to at least 150.  Setting pred_flank
too low will also limit how far MAKER  will walk out along the edges initial
alignments during the polishing step (exonerate).  So setting it too low may
also be causing you to lose some EST and protein alignments.

--Carson


From:  Benjamin Rubin <brubin at fieldmuseum.org>
Date:  Monday, August 26, 2013 2:20 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Unexpected results with correct_est_fusion

Hello developers,

I am using MAKER 2.28 to annotate an ant genome. I provide protein sequence
evidence from all seven of the other sequenced ant genomes and a de novo
assembled transcriptome as EST evidence. I assembled the transcriptome using
Trinity with the jaccard_clip option turned on to reduce gene fusions.
Despite using this set of hopefully non-fused ESTs, I still have substantial
fusion problems with the final annotation. Therefore, I reduced pred_flank
to 100 and turned on correct_est_fusion. However, correct_est_fusion leads
to the prediction of a much smaller number of genes (~5,000 instead of
~14,000). I am initially training both SNAP and Augustus using CEGMA genes
and then retraining based on the first round of annotation. Both rounds of
annotation yield the same low number (~5,000) of genes. It may also be worth
mentioning that the number of exons is also far lower when using
correct_est_fusion (~26,000 instead of ~90,000).

Is this the expected behavior of correct_est_fusion? I was surprised that it
reduced the predicted number of genes by such a large margin. I am concerned
that I am using it incorrectly. Do you have any other suggestions for
reducing gene merging?

Thanks,
Ben

-- 
_____________________________________________________
Benjamin ER Rubin
PhD Candidate
Committee on Evolutionary Biology
University of Chicago
http://www.moreaulab.org/Benjamin_Rubin.html

Division of Insects
Zoology Department
Field Museum of Natural History
1400 South Lake Shore Drive
Chicago, IL 60605
USA
Office: (312) 665-7776 <tel:%28312%29%20665-7776>
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