add annotation features to BSgenome or txdb package
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Didi ▴ 10
@didi-10905
Last seen 11 weeks ago
Spain

Hi,

Is it possible to add annotation features to a BSgenome package or a txdb package in case there isn't an orgDB package for non model organisms?

Is it easy to do it?

Thanks a lot.

Regards,

D.

bsgenome txdb annotation orgdb • 1.2k views
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@herve-pages-1542
Last seen 1 hour ago
Seattle, WA, United States

Hi D.,

If there is no OrgDb package for your non model organism, and you need one, then I guess you'd want to make one. Not clear to me why you'd want to put these annotations in a BSgenome data package. These packages are meant for the genome sequences. Could you clarify what you are trying to do? Also what kind of annotation you have access to for your non model organism? Note that if they are in a GTF or GFF file, you can import them as a TxDb object by just calling makeTxDbFromGFF() on the file.

H.

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Entering edit mode
Didi ▴ 10
@didi-10905
Last seen 11 weeks ago
Spain

I have GTF and GFF files. I imported them as a TxDb object and it works.

Thanks a lot.

Regards,

D.