We have to re-generate these packages - there was an error that excluded 65
genes (total) from nine of the species. They will be available early next week.
Sorry for the delay!
Best,
Jim
-Original Message-
From: Bioc-devel On Behalf Of Kern, Lori via
Bioc-devel
Sent: Thursday, Marc
tx_name
> |
>[1] chrM 3230-3304 + |252881 ENST0386347.1
>---
>seqinfo: 439 sequences (1 circular) from an unspecified genome; no
> seqlengths
>
>
> As with most human endeavors, the weight of history hangs heavy
an I have tried many
(many) times to get affy removed in lieu of oligo, to no avail.
From: Tim Triche, Jr.
Sent: Thursday, March 28, 2024 10:40 AM
To: James W. MacDonald
Cc: Vincent Carey ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now
available
1 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 Messa
yep, looks like that's the problem
I wonder why it doesn't have a CDS chromosome in ENSEMBL? That's a bit
nuts.
It is indeed indexed to MT in the canonical ENSEMBL database:
https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG0198727;r=MT:14747-15887;t=ENST0361789
--t
On Thu,
2024 10:00 AM
To: Tim Triche, Jr.
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now
available
winging it here tim
> select(Homo.sapiens, keys="ENSG0198727", keytype="ENSEMBL",
columns=c("GENENAME", "GENEID&quo
winging it here tim
> select(Homo.sapiens, keys="ENSG0198727", keytype="ENSEMBL",
columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL"))
'select()' returned 1:1 mapping between keys and columns
ENSEMBL GENENAME SYMBOL CDSCHROM GENEID
1 ENSG0198727 cytochrome b CYTB4
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
