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

[Christian Arnold]

Dear Vincent and others,

thanks for the reply! Irrespective of whether a different OrgDb is
required, the name itself suggested that there "should be" also
corresponding OrgDb and TxDb packages. I can build one on my own, I see,
is there anyone who works on providing the TxDB object for Bioc?

I am also asking this because the T2T people specifically provide an
"updated" gene annotation dataset which may differ from what's inside
OrgDb and may be incompatible with? See here:
https://github.com/marbl/CHM13:

/JHU RefSeqv110 + Liftoff v5.1
<https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v2.0_RefSeq_Liftoff_v5.1.gff3.gz>:
This containscuratedannotations of the ampliconic genes on the Y
chromosome, correcting annotation errors in GENCODEv35 CAT/Liftoff and
RefSeqv110 annotation. Additional copies found in T2T-Y were annotated
to the closest available gene in RefSeq, allowing multiple genes to have
the same common name. This file has been modified to correct special
character issues from the original file.
/

/
/

For ArchR, I tried to understand how one can create a new genome by
checking here:
https://www.archrproject.com/bookdown/getting-set-up.html. There, they
explicitly mention the TxDb and OrgDb objects that are needed for
building a custom genome. There seems to be another option when both or
any of these 2 is not available ("Alternatively, if you dont have
a|TxDb|and|OrgDb|object, you can create a|geneAnnotation|object from the
following information" ), but I first tried to do it the easy way as I
want to properly embed it in a pipeline with as little "custom" code as
possible.


Thanks,
Christian




On 11/12/2023 15:30, Vincent Carey wrote:
> 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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