User: creasyt

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creasyt0
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Posts by creasyt

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Comment: C: Translation Error in predictCoding() for VariantAnnotation
... Hi Herve, I saw that, too. However, these are not start codons which is why I brought it up. Plus, I think that setting GENETIC_CODE is only to translate the nucleotide sequence. I *think* the codons are translated in another function later on in a separate function. I noticed that the only time sa ...
written 10 days ago by creasyt0
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Comment: C: Translation Error in predictCoding() for VariantAnnotation
... Sorry, the "**TTG**" was a mistake. I removed them from the post. I've added some code that I used to generate the custom txdb object which is for a RSV virus, the gff3 data, the fasta sequence, and the sessionInfo(). Let me know what else you need. ...
written 21 days ago by creasyt0
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Translation Error in predictCoding() for VariantAnnotation
... Hi, I'm noticing what appears to be an incorrect translation of a codon with predictCoding(). It's somewhat difficult to see but below is output of all nonsynonymous amino acid changes. However, variant 3 at bp 1002 shows an M for TTG rather than an L. Is this a bug? Clearly TTG is an L in the stan ...
variantannotation written 23 days ago by creasyt0 • updated 15 days ago by Hervé Pagès ♦♦ 12k

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