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Question: add annotation features to BSgenome or txdb package
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gravatar for Didi
4 months ago by
Didi10
Didi10 wrote:

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.

ADD COMMENTlink modified 3 months ago • written 4 months ago by Didi10
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gravatar for Hervé Pagès
3 months ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

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.

ADD COMMENTlink written 3 months ago by Hervé Pagès ♦♦ 13k
0
gravatar for Didi
3 months ago by
Didi10
Didi10 wrote:

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

Thanks a lot.

Regards,

D.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Didi10
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