[Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available
Tim Triche, Jr.
t|m@tr|che @end|ng |rom gm@||@com
Thu Mar 28 15:40:24 CET 2024
is this an argument in favor of using ENSEMBL gene and transcript IDs
rather than ENTREZ or UCSC? Or just changing the way that the databases
are keyed? There really ought not to be transcripts for a gene on a
different chromosome from the gene, although the MHC and KIR loci (with alt
contigs) somewhat force the issue for that. (we could discuss graph
genomes here, but we aren't going to do that, because all
gene->transcript->contig mappings start to break)
Omission of an entire chromosome seems... bad? Regardless of the technical
reason why. There are arguments in favor of e.g. gene -> transcript ->
contig where each relationship is potentially 1:many, but if chrM can't be
sorted out then I am dubious that more complicated mappings can be
efficiently handled. chrM is particularly weird in that it can have
multiple haplotypes (i.e. contigs) even within the same cell, but at some
point, simplifications are merited
--t
On Thu, Mar 28, 2024 at 10:12 AM James W. MacDonald <jmacdon using uw.edu> wrote:
> As well as
>
> > subsetByOverlaps(transcripts(Homo.sapiens), GRanges("chrM:1-16569"))
> 'select()' returned 1:1 mapping between keys and columns
> GRanges object with 37 ranges and 2 metadata columns:
> seqnames ranges strand | TXID TXNAME
> <Rle> <IRanges> <Rle> | <IntegerList> <CharacterList>
> [1] chrM 577-647 + | 252799 ENST00000387314.1
> [2] chrM 648-1601 + | 252800 ENST00000389680.2
> [3] chrM 1602-1670 + | 252801 ENST00000387342.1
> [4] chrM 1671-3229 + | 252802 ENST00000387347.2
> [5] chrM 3230-3304 + | 252803 ENST00000386347.1
> ... ... ... ... . ... ...
> [33] chrM 5826-5891 - | 252831 ENST00000387409.1
> [34] chrM 7446-7514 - | 252832 ENST00000387416.2
> [35] chrM 14149-14673 - | 252833 ENST00000361681.2
> [36] chrM 14674-14742 - | 252834 ENST00000387459.1
> [37] chrM 15956-16023 - | 252835 ENST00000387461.2
> -------
> seqinfo: 711 sequences (1 circular) from hg38 genome
>
> However
>
> > subsetByOverlaps(transcriptsBy(Homo.sapiens), GRanges("chrM:1-16569"))
> GRangesList object of length 0:
> <0 elements>
>
> And
>
> > subsetByOverlaps(transcripts(Homo.sapiens, columns =
> c("GENEID","SYMBOL")), GRanges("chrM:1-16569"))
> 'select()' returned 1:1 mapping between keys and columns
> GRanges object with 37 ranges and 2 metadata columns:
> seqnames ranges strand | GENEID SYMBOL
> <Rle> <IRanges> <Rle> | <CharacterList> <CharacterList>
> [1] chrM 577-647 + | <NA> <NA>
> [2] chrM 648-1601 + | <NA> <NA>
> [3] chrM 1602-1670 + | <NA> <NA>
> [4] chrM 1671-3229 + | <NA> <NA>
> [5] chrM 3230-3304 + | <NA> <NA>
> ... ... ... ... . ... ...
> [33] chrM 5826-5891 - | <NA> <NA>
> [34] chrM 7446-7514 - | <NA> <NA>
> [35] chrM 14149-14673 - | <NA> <NA>
> [36] chrM 14674-14742 - | <NA> <NA>
> [37] chrM 15956-16023 - | <NA> <NA>
> -------
> seqinfo: 711 sequences (1 circular) from hg38 genome
>
> Everything is mapped via the GENEID, and if you query the UCSC genome
> browser for hg38/knownGene, asking for gene name, known gene ID and gene
> symbol, you will get the first and last but not the middle.
>
>
>
> -----Original Message-----
> From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Vincent
> Carey
> Sent: Thursday, March 28, 2024 10:00 AM
> To: Tim Triche, Jr. <tim.triche using gmail.com>
> Cc: bioc-devel using r-project.org
> Subject: Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now
> available
>
> winging it here tim
>
> > select(Homo.sapiens, keys="ENSG00000198727", keytype="ENSEMBL",
> columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL")) 'select()' returned
> 1:1 mapping between keys and columns
> ENSEMBL GENENAME SYMBOL CDSCHROM GENEID
> 1 ENSG00000198727 cytochrome b CYTB <NA> 4519
> > select(Homo.sapiens, keys= "MTCYBP1", keytype="SYMBOL",
> columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL")) 'select()' returned
> 1:1 mapping between keys and columns
> SYMBOL GENENAME CDSCHROM GENEID
> 1 MTCYBP1 MT-CYB pseudogene 1 <NA> 100499418
>
> relevant?
>
> On Thu, Mar 28, 2024 at 9:17 AM Tim Triche, Jr. <tim.triche using gmail.com>
> wrote:
>
> > Hi Lori and fellow maintainers,
> >
> > I had a strange experience yesterday where I pulled down genes and
> > transcripts from Homo.sapiens, only to discover that all mitochondrial
> > encoded genes (MT-CYB, MT-CO2, etc) were missing.
> >
> > Is there an historical reason why this is so? Obviously these
> > transcripts are physiologically important, but beyond that, they’re
> > also used all the time in single cell sequencing to estimate viability.
> >
> > Best,
> >
> > --t
> >
> > > On Mar 28, 2024, at 8:47 AM, Kern, Lori via Bioc-devel <
> > bioc-devel using r-project.org> wrote:
> > >
> > > Hello Bioconductor community,
> > >
> > > The newest db0, OrgDb, and TxDb annotation packages for the upcoming
> > Bioconductor 3.19 release are up and available for download in the
> > devel version of Bioconductor.
> > >
> > > The deadline for submitting contributed annotation packages will be
> > Wednesday April 17 th.
> > >
> > > The new db0 packages are:
> > >
> > > anopheles.db0_3.19.0.tar.gz
> > > arabidopsis.db0_3.19.0.tar.gz
> > > bovine.db0_3.19.0.tar.gz
> > > canine.db0_3.19.0.tar.gz
> > > chicken.db0_3.19.0.tar.gz
> > > chimp.db0_3.19.0.tar.gz
> > > ecoliK12.db0_3.19.0.tar.gz
> > > ecoliSakai.db0_3.19.0.tar.gz
> > > fly.db0_3.19.0.tar.gz
> > > human.db0_3.19.0.tar.gz
> > > malaria.db0_3.19.0.tar.gz
> > > mouse.db0_3.19.0.tar.gz
> > > pig.db0_3.19.0.tar.gz
> > > rat.db0_3.19.0.tar.gz
> > > rhesus.db0_3.19.0.tar.gz
> > > worm.db0_3.19.0.tar.gz
> > > xenopus.db0_3.19.0.tar.gz
> > > yeast.db0_3.19.0.tar.gz
> > > zebrafish.db0_3.19.0.tar.gz
> > >
> > > The new OrgDb packages are:
> > >
> > > GO.db_3.19.0.tar.gz
> > > org.Ag.eg.db_3.19.0.tar.gz
> > > org.At.tair.db_3.19.0.tar.gz
> > > org.Bt.eg.db_3.19.0.tar.gz
> > > org.Ce.eg.db_3.19.0.tar.gz
> > > org.Cf.eg.db_3.19.0.tar.gz
> > > org.Dm.eg.db_3.19.0.tar.gz
> > > org.Dr.eg.db_3.19.0.tar.gz
> > > org.EcK12.eg.db_3.19.0.tar.gz
> > > org.EcSakai.eg.db_3.19.0.tar.gz
> > > org.Gg.eg.db_3.19.0.tar.gz
> > > org.Hs.eg.db_3.19.0.tar.gz
> > > org.Mm.eg.db_3.19.0.tar.gz
> > > org.Mmu.eg.db_3.19.0.tar.gz
> > > org.Pt.eg.db_3.19.0.tar.gz
> > > org.Rn.eg.db_3.19.0.tar.gz
> > > org.Sc.eg.db_3.19.0.tar.gz
> > > org.Ss.eg.db_3.19.0.tar.gz
> > > org.Xl.eg.db_3.19.0.tar.gz
> > > Orthology.eg.db_3.19.0.tar.gz
> > > PFAM.db_3.19.0.tar.gz
> > >
> > > The new TxDb packages are:
> > >
> > > TxDb.Hsapiens.UCSC.hg38.refGene_3.19.0.tar.gz
> > > TxDb.Mmusculus.UCSC.mm39.refGene_3.19.0.tar.gz
> > >
> > > Thank you
> > >
> > >
> > > Lori Shepherd - Kern
> > >
> > > Bioconductor Core Team
> > >
> > > Roswell Park Comprehensive Cancer Center
> > >
> > > Department of Biostatistics & Bioinformatics
> > >
> > > Elm & Carlton Streets
> > >
> > > Buffalo, New York 14263
> > >
> > >
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