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

[Vincent Carey]

Thanks Jim, I tend to agree with you.  Christian, I had a look at ArchR but
could not tell where the
system contacts the Bioc annotation elements.  Can you give some hints?
I'd like to be able to
verify compatibility.

On Mon, Dec 11, 2023 at 9:19 AM James W. MacDonald <jmacdon using uw.edu> wrote:

> I don't believe a different OrgDb is required. The OrgDb package is meant
> to provide annotations for genes such as gene symbol or GO term, etc, which
> are orthogonal to the sequence of the genome, so the current version should
> suffice.
>
> -----Original Message-----
> From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Vincent
> Carey
> Sent: Sunday, December 10, 2023 1:44 PM
> To: Christian Arnold <chrarnold using web.de>
> Cc: bioc-devel using r-project.org
> Subject: Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects
>
> Good question.  I believe these will be forthcoming soon.  In the mean
> time you can create your own.  See, for example
>
>
> https://urldefense.com/v3/__https://github.com/vjcitn/BiocT2T/blob/devel/inst/scripts/makeTxDb.R__;!!K-Hz7m0Vt54!ixhBX1kJeZc-9e3gcVgd5OOsvXj8vYfmUZphWadsaXZmdIMiLYcLZEGkJmZhkFTxT-wXY5c_hr0C9adMcpWaIEw$
>
> It's an active area so you can pull a gff file from
> https://urldefense.com/v3/__https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T*CHM13*assemblies*annotation*__;Ly8vLw!!K-Hz7m0Vt54!ixhBX1kJeZc-9e3gcVgd5OOsvXj8vYfmUZphWadsaXZmdIMiLYcLZEGkJmZhkFTxT-wXY5c_hr0C9adM7PNUeks$
> 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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>
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