[maker-devel] Overlapping Gene Models

[Robert Auber]

Hello MAKER devs,

I have been attempting to run MAKER2 (2.31.10) on an assembly of a
Haptophyte genome (~160MB). After running four rounds of MAKER2 (details of
pipeline shown below in diagram), I obtained a reasonable set of gene calls
with great BUSCO completeness and AED scores. However, ~11,00 of the
~42,000 gene models have an overlap in their CDS with another gene model's
CDS. There are no overlaps on the same strand (thank goodness), and I have
read on the google group threads that cases of overlapping gene models on
opposite stands can occur, but I have not seen it to this extent. Below are
some examples of some overlapping models. Interestingly, some of these
models have unique exon structures compared to their overlapping partner.

[image: Screen Shot 2019-11-05 at 12.29.53 PM.png]

[image: Screen Shot 2019-11-05 at 12.31.17 PM.png]

I have tried extensively to filter out these overlapping gene models by
employing different thresholds such as AED/eAED scores and amount of
est/prot/etc support but the majority of these genes seem to have a minimal
difference in AED scores and have multiple lines of support. The only trend
I have pulled from the output is that 40% of the overlapping genes are
labeled as 'snap' or 'snap processed' genes, though again most of these do
have support from other sources according to the gff3. I would be very
appreciative of any thought or input you may have on these overlapping gene
models. If you need more metrics or information on what I did when running
MAKER2 to help clarify anything, please let me know!

[image: MAKER_PIPELINE_V3_maker_devs.png]
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