[maker-devel] evidence of transcript assembly

[Quanwei Zhang]

Hello:

I am using Maker2 to do gene annotation on a new rodent species. I have
found some published RNA-seq data and there are selected open reading
frames. Generally they get the transcript assembly through Trinity, after
that they mapped the raw  transcript assemblies to mouse genome and
selected those with full coverage of mouse genes or part coverage. I have a
questions about the evidence of transcript assembly for Marker. Which do
you think is a best choice as evidences to Maker2?
(1) All the Trinity transcript assemblies?
(2) Trinity transcript assemblies that fully cover the mouse genes?
(3) Trinity transcript assemblies either fully or partly cover the mouse
genes?

Many thanks

Best
Quanwei
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