Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects
FWIW I've documented the process of making a TxDb object for
T2T-CHM13v2.0 there:
https://github.com/Bioconductor/GenomicFeatures/issues/65
Please comment there for any follow-up.
Note that we're considering wrapping this is an TxDb package that we'll
make available to the community. It's a work-in-progress.
Thanks!
H.
On 12/12/23 07:29, James W. MacDonald wrote:
> Hi Christian,
>
> This conversation is off-topic, both for this listserv (it’s meant to help
> people developing Bioconductor packages) and for the support site (which is
> meant to help people with (again), Bioconductor packages. I’ll answer your
> questions one more time, but if you have other questions, please move to
> biostars.org, or just ask the ArchR people directly, since it’s their package.
>
> I believe you are misinterpreting what an OrgDb is intended to provide. There
> is no positional data in an OrgDb, and what the CHM13 project has done is
> completely positional (what data are provided in the ‘Gene Annotation’
> section of the CHM13 Github are all GFF files, which are meant to provide
> positional information of genes on a genome).
>
> The OrgDb package provides functional and within-annotation mappings. You can
> map an NCBI Gene ID to Ensembl, or to the HGNC gene symbol, or a GO term,
> etc. For example, I can map Gene symbol P53 to NCBI Gene ID 7157, or its
> UniProt symbol K7PPA8. If the new genome build says P53 has moved to a new
> genomic position, that has no affect on what UniProt thinks the ID for that
> gene’s protein should be, or what ID NCBI uses, or what GO terms are appended
> to that gene. Functionally it’s the same gene. We just might think it is
> located in a different place in the genome.
>
> The difference between CHM13 and GRCh38 is not materially different from the
> difference between GRCh37 and GRCh38 (they represent the current knowledge of
> the genome at a point in time), and while we supply TxDb packages for GRCh38
> and GRCh37 (and variants based on NCBI’s mappings as well as Ensembl’s
> mappings), we have never supplied more than one human OrgDb package, because
> the positional and functional information are orthogonal.
>
> It seems pretty simple to make what you need though.
>
>> library(GenomicAlignments)
>> tx <-
>> makeTxDbFromGFF(https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz)
> Import genomic features from the file as a GRanges object ... trying URL
> 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz'
> Content type 'application/x-gzip' length 79009538 bytes (75.3 MB)
> downloaded 75.3 MB
>
> OK
> Prepare the 'metadata' data frame ... OK
> Make the TxDb object ... OK
> Warning messages:
> 1: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID, :
>some transcripts have no
>"transcript_id" attribute ==>
>their name ("tx_name" column in
>the TxDb object) was set to NA
> 2: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID, :
>the transcript names ("tx_name"
>column in the TxDb object)
>imported from the
>"transcript_id" attribute are
>not unique
> 3: In .find_exon_cds(exons, cds) : The following transcripts have
>exons that contain more than one
>CDS (only the first CDS was kept
>for each exon):
>rna-NM_001134939.1,
>rna-NM_001172437.2,
>rna-NM_001184961.1,
>rna-NM_001301020.1,
>rna-NM_001301302.1,
>rna-NM_001301371.1,
>rna-NM_002537.3,
>rna-NM_004152.3,
>rna-NM_015068.3, rna-NM_016178.2
>> tx
> TxDb object:
> # Db type: TxDb
> # Supporting package: GenomicFeatures
> # Data
> source:https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz
> # Organism: NA
> # Taxonomy ID: NA
> # miRBase build ID: NA
> # Genome: NA
> # Nb of transcripts: 188205
> # Db created by: GenomicFeatures package from Bioconductor
> # Creation time: 2023-12-12 10:17:34 -0500 (Tue, 12 Dec 2023)
> # GenomicFeatures version at creation time: 1.54.1
> # RSQLite version at creation time: 2.3.1
> # DBSCHEMAVERSION: 1.2
>
> genomeAnnotation <-
> createGenomeAnnotation(BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0)
> geneAnnotation <- createGeneAnnotation(TxDb = tx, OrgDb = org.Hs.eg.db)
>
>
> Best,
>
> Jim
>
> From: Christian Arnold
> Sent: Tuesday, December 12, 2023 9:35 AM
> To: Vincent Carey; James W.
> MacDonald
> Cc:bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Miss
Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects
Hi Christian,
This conversation is off-topic, both for this listserv (it’s meant to help
people developing Bioconductor packages) and for the support site (which is
meant to help people with (again), Bioconductor packages. I’ll answer your
questions one more time, but if you have other questions, please move to
biostars.org, or just ask the ArchR people directly, since it’s their package.
I believe you are misinterpreting what an OrgDb is intended to provide. There
is no positional data in an OrgDb, and what the CHM13 project has done is
completely positional (what data are provided in the ‘Gene Annotation’ section
of the CHM13 Github are all GFF files, which are meant to provide positional
information of genes on a genome).
The OrgDb package provides functional and within-annotation mappings. You can
map an NCBI Gene ID to Ensembl, or to the HGNC gene symbol, or a GO term, etc.
For example, I can map Gene symbol P53 to NCBI Gene ID 7157, or its UniProt
symbol K7PPA8. If the new genome build says P53 has moved to a new genomic
position, that has no affect on what UniProt thinks the ID for that gene’s
protein should be, or what ID NCBI uses, or what GO terms are appended to that
gene. Functionally it’s the same gene. We just might think it is located in a
different place in the genome.
The difference between CHM13 and GRCh38 is not materially different from the
difference between GRCh37 and GRCh38 (they represent the current knowledge of
the genome at a point in time), and while we supply TxDb packages for GRCh38
and GRCh37 (and variants based on NCBI’s mappings as well as Ensembl’s
mappings), we have never supplied more than one human OrgDb package, because
the positional and functional information are orthogonal.
It seems pretty simple to make what you need though.
> library(GenomicAlignments)
> tx <-
> makeTxDbFromGFF(https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz)
Import genomic features from the file as a GRanges object ... trying URL
'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz'
Content type 'application/x-gzip' length 79009538 bytes (75.3 MB)
downloaded 75.3 MB
OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID, :
some transcripts have no
"transcript_id" attribute ==>
their name ("tx_name" column in
the TxDb object) was set to NA
2: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID, :
the transcript names ("tx_name"
column in the TxDb object)
imported from the
"transcript_id" attribute are
not unique
3: In .find_exon_cds(exons, cds) : The following transcripts have
exons that contain more than one
CDS (only the first CDS was kept
for each exon):
rna-NM_001134939.1,
rna-NM_001172437.2,
rna-NM_001184961.1,
rna-NM_001301020.1,
rna-NM_001301302.1,
rna-NM_001301371.1,
rna-NM_002537.3,
rna-NM_004152.3,
rna-NM_015068.3, rna-NM_016178.2
> tx
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source:
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz
# Organism: NA
# Taxonomy ID: NA
# miRBase build ID: NA
# Genome: NA
# Nb of transcripts: 188205
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2023-12-12 10:17:34 -0500 (Tue, 12 Dec 2023)
# GenomicFeatures version at creation time: 1.54.1
# RSQLite version at creation time: 2.3.1
# DBSCHEMAVERSION: 1.2
genomeAnnotation <- createGenomeAnnotation(BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0)
geneAnnotation <- createGeneAnnotation(TxDb = tx, OrgDb = org.Hs.eg.db)
Best,
Jim
From: Christian Arnold
Sent: Tuesday, December 12, 2023 9:35 AM
To: Vincent Carey ; James W. MacDonald
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects
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
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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 anyon
Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects
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 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 On Behalf Of
> Vincent Carey
> Sent: Sunday, December 10, 2023 1:44 PM
> To: Christian Arnold
> Cc: bioc-devel@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@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
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc
> >
> -devel__;!!K-Hz7m0Vt54!ixhBX1kJeZc-9e3gcVgd5OOsvXj8vYfmUZphWadsaXZmdIM
> > iLYcLZEGkJmZhkFTxT-wXY5c_hr0C9adMOtbUwTc$
> >
>
> --
> The information in this e-mail is intended only for the
> ...{{dropped:18}}
>
> ___
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>
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>
>
>
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Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects
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 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 On Behalf Of Vincent
> Carey
> Sent: Sunday, December 10, 2023 1:44 PM
> To: Christian Arnold
> Cc: bioc-devel@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@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
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc
> > -devel__;!!K-Hz7m0Vt54!ixhBX1kJeZc-9e3gcVgd5OOsvXj8vYfmUZphWadsaXZmdIM
> > iLYcLZEGkJmZhkFTxT-wXY5c_hr0C9adMOtbUwTc$
> >
>
> --
> The information in this e-mail is intended only for th...{{dropped:29}}
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Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects
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 On Behalf Of Vincent Carey
Sent: Sunday, December 10, 2023 1:44 PM
To: Christian Arnold
Cc: bioc-devel@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@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
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc
> -devel__;!!K-Hz7m0Vt54!ixhBX1kJeZc-9e3gcVgd5OOsvXj8vYfmUZphWadsaXZmdIM
> iLYcLZEGkJmZhkFTxT-wXY5c_hr0C9adMOtbUwTc$
>
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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://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@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
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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[Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects
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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
