[Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects

[Vincent Carey]

Good question.  I believe these will be forthcoming soon.  In the mean time
you can
create your own.  See, for example

https://github.com/vjcitn/BiocT2T/blob/devel/inst/scripts/makeTxDb.R

It's an active area so you can pull a gff file from
https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T/CHM13/assemblies/annotation/
and adjust the code noted above for the TxDb.

For the org.db I have to get back to you.

On Sun, Dec 10, 2023 at 12:06 PM Christian Arnold via Bioc-devel <
bioc-devel using r-project.org> wrote:

> Hello, I am working with the new human T2T-CHM13v2.0  assembly and while
> a BSgenome package already exists
> (BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0), I could not find the
> corresponding TxDb and OrgDb packages. Is there any information when
> they may also become available so it is easier to work with the new
> genome for packages like ArchR, which support a custom genome but need
> these standard annotation packages for their creation?
>
>
> Thanks a lot for any information regarding this!
>
> Best, Christian
>
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