[maker-devel] Unexpected results with correct_est_fusion

[Benjamin Rubin]

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
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