User: erik.kastman

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erik.kastman10
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Posts by erik.kastman

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Comment: C: Eukaryotic gene annotation transfer tools
... 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? ...
written 12 months ago by erik.kastman10
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LiftOver Building a pseudo-molecule
... I'm attempting to follow this interesting [yeast genome][1] paper, which took newly sequenced assemblies, used the UCSC liftOver pipeline to line them up to a reference, and then create a pseudo-molecule that matched the primary yeast reference: > Each de novo assembly was scaffolded against the ...
liftover written 2.4 years ago by erik.kastman10
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Eukaryotic gene annotation transfer tools
... 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 the ...
transfer annotation eukaryotic written 4.7 years ago by erik.kastman10
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Answer: A: How do I get a list of RefSeq from Assembly in Entrez?
... I'm not very familiar with EFetch, but it seems to me that the assembly database may not be fully implemented. If you look at the EFetch help, there aren't any options for db=assembly: Additionally, there are no direct links to download an assembly from the ncbi site, anyway. For an example, check ...
written 5.2 years ago by erik.kastman10 • updated 11 months ago by RamRS30k

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Popular Question 2.3 years ago, created a question with more than 1,000 views. For Eukaryotic gene annotation transfer tools

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