Question: Eukaryotic gene annotation transfer tools
1
gravatar for erik.kastman
3.8 years ago by
erik.kastman10
United States
erik.kastman10 wrote:

I'm trying to transfer annotations from an ancestral fungal genome to newly sequenced mutants, and for both speed and consistency I'd like to be able to transfer annotations from the ancestor to syntenic regions on the mutants. I've looked at Rapid Annotation Transfer Tool (RATT) and tried using their eukaryotic codon settings, but the coverage on each of the contigs is spotty - it seems to work well for the first 3rd of each contig and then fail for the remaining 2/3's, while claiming to complete successfully without any errors.

Does anyone have suggestions on other tools for annotation transfer / liftover that are explicitly designed to be used for eukaryotic genomes? At current the omictools directory only lists new annotation pipelines and not transfers. Thanks in advance,

Erik

eukaryotic annotation transfer • 1.3k views
ADD COMMENTlink written 3.8 years ago by erik.kastman10

Did you find the problem?

ADD REPLYlink written 22 days ago by m.t.lorenc0

IIRC I think I did end up getting RATT to work, but I don't remember what the solution was, and I don't think I ever found better alternatives. I'd be curious to hear if you find one; are you having the same incompleteness problem?

ADD REPLYlink written 22 days ago by erik.kastman10
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