Hi Raymond, Tim,
TxDb.Hsapiens.UCSC.hg19.knownGene got updated last week in BioC 3.22 to reflect
the current state of UCSC track hg19.knownGene, but the new version of the
package (3.22.0) does not carry the correct circularity flag for chrMT, only
for chrM. This is on our end and will be addressed shortly.
List of packages affected by this: annotatr, decompTumor2Sig, GenomicFeatures,
gmapR, MutationalPatterns, OrganismDbi, ProteoDisco, and VariantTools.
Sorry for the inconvenience.
Best,
H.
On 13/10/2025 07:24, Raymond Cavalcante wrote:
I'm sorry, I must have missed the moment where chrM and chrMT were both
included, or they always were and I didn't notice it. To put a finer point
on this issue, the seqinfo from Txdb is inconsistent with that from Seqinfo:
txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
tx_gr = transcripts(txdb, columns = c('TXID','GENEID','TXNAME'))
seqinfo(tx_gr)[c('chrM','chrMT')]
Seqinfo object with 2 sequences (1 circular) from hg19 genome:
seqnames seqlengths isCircular genome
chrM 16571 TRUE hg19
chrMT 16569 FALSE hg19
chrMT is circular from Seqinfo but not from TxDb.
Thanks,
Raymond
--------------------
Raymond Cavalcante, PhD
Bioinformatics Analyst
Epigenomics Core and Bioinformatics Core
Biomedical Research Core Facilities
University of Michigan Medical School
[email protected]
[email protected]
On Sun, Oct 12, 2025 at 10:57 AM Tim Triche, Jr. <[email protected]>
wrote:
chrM is the broken old hg19 mitogenome
chrMT is rCRS, same as hg38 chrM
--t
On Oct 12, 2025, at 12:30 PM, Raymond Cavalcante <[email protected]>
wrote:
Hi,
I was testing the annotatr package after fixing the ggplot2 v4 stuff,
but I
got an error in my vignette build and discovered what I think is an error
in the result of Seqinfo::seqinfo(genome = 'hg19').
There are two mitochondrial chromosomes for hg19. This causes some
downstream issues when merging hg19 GRanges.
Seqinfo::Seqinfo(genome='hg19')[c('chrM', 'chrMT')]
Seqinfo object with 2 sequences (2 circular) from hg19 genome:
seqnames seqlengths isCircular genome
chrM 16571 TRUE hg19
chrMT 16569 TRUE hg19
I checked hg38 on a lark and it appears correct.
Seqinfo::Seqinfo(genome='hg38')[c('chrM', 'chrMT')]
Seqinfo object with 2 sequences (1 circular) from 2 genomes (hg38, NA):
seqnames seqlengths isCircular genome
chrM 16569 TRUE hg38
chrMT NA NA <NA>
I'm using 0.99.2 of Seqinfo in a Bioconductor devel Docker image.
My session info:
devtools::session_info()
─ Session info
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.5.1 (2025-06-13)
os Ubuntu 24.04.3 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2025-10-12
pandoc 3.8.1 @ /usr/bin/pandoc
quarto 1.7.32 @ /usr/local/bin/quarto
─ Packages
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
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Thanks!
--------------------
Raymond Cavalcante, PhD
Bioinformatics Analyst
Epigenomics Core and Bioinformatics Core
Biomedical Research Core Facilities
University of Michigan Medical School
[email protected]
[email protected]
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