[maker-devel] MAKER chooser algorithm

[Timo Metz]

Hey,

I am working on the improvement of an already existing annotation. I could
find that sometimes MAKER would split or merge genes where it intuitively
does not look correct when looking at the evidence. Please find two
examples attached. The first track is the old annotation, the second track
the new annotation, then there is RNA-seq data, proteins, repeats, snap
prediction, augustus prediction. It is visible, that in both cases the
evidence supports two genes, and one gene predictor in each case tends to
create one gene where the other one creates two genes. I do not understand
why in this case the gene is merged, if evidence and also one ab initio
prediction support rather two genes. Are there any suggestions on how to
solve this?

best
Timo
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