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
> > abind 1.4-8 2024-09-12 [1] RSPM (R
> > 4.5.0)
> > AnnotationDbi * 1.71.1 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > AnnotationHub 3.99.6 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > VP annotatr * 1.35.1 2025-05-13 [?]
> > Bioconductor 3.22 (R 4.5.0) (on disk 1.35.0)
> > Biobase * 2.69.1 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > BiocFileCache 2.99.6 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > BiocGenerics * 0.55.3 2025-10-09 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > BiocIO 1.19.0 2025-04-15 [1]
> > Bioconductor 3.22 (R 4.5.0)
> > BiocManager 1.30.26 2025-06-05 [1] CRAN (R
> > 4.5.1)
> > BiocParallel 1.43.4 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > BiocVersion 3.22.0 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > Biostrings 2.77.2 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > bit 4.6.0 2025-03-06 [1] RSPM (R
> > 4.5.0)
> > bit64 4.6.0-1 2025-01-16 [1] RSPM (R
> > 4.5.0)
> > bitops 1.0-9 2024-10-03 [1] RSPM (R
> > 4.5.0)
> > blob 1.2.4 2023-03-17 [1] RSPM (R
> > 4.5.0)
> > brio 1.1.5 2024-04-24 [1] RSPM (R
> > 4.5.0)
> > BSgenome 1.77.2 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > cachem 1.1.0 2024-05-16 [1] RSPM (R
> > 4.5.0)
> > cli 3.6.5 2025-04-23 [1] RSPM (R
> > 4.5.0)
> > codetools 0.2-20 2024-03-31 [2] CRAN (R
> > 4.5.1)
> > crayon 1.5.3 2024-06-20 [1] RSPM (R
> > 4.5.0)
> > curl 7.0.0 2025-08-19 [1] RSPM (R
> > 4.5.0)
> > DBI 1.2.3 2024-06-02 [1] RSPM (R
> > 4.5.0)
> > dbplyr 2.5.1 2025-09-10 [1] RSPM (R
> > 4.5.0)
> > DelayedArray 0.35.3 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > desc 1.4.3 2023-12-10 [1] RSPM (R
> > 4.5.0)
> > devtools 2.4.6 2025-10-03 [1] RSPM (R
> > 4.5.0)
> > dplyr 1.1.4 2023-11-17 [1] RSPM (R
> > 4.5.0)
> > ellipsis 0.3.2 2021-04-29 [1] RSPM (R
> > 4.5.0)
> > farver 2.1.2 2024-05-13 [1] RSPM (R
> > 4.5.0)
> > fastmap 1.2.0 2024-05-15 [1] RSPM (R
> > 4.5.0)
> > filelock 1.0.3 2023-12-11 [1] RSPM (R
> > 4.5.0)
> > fs 1.6.6 2025-04-12 [1] RSPM (R
> > 4.5.0)
> > generics * 0.1.4 2025-05-09 [1] RSPM (R
> > 4.5.0)
> > GenomeInfoDb 1.45.12 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > GenomicAlignments 1.45.4 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > GenomicFeatures * 1.61.6 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > GenomicRanges * 1.61.5 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > ggplot2 4.0.0 2025-09-11 [1] RSPM (R
> > 4.5.0)
> > glue 1.8.0 2024-09-30 [1] RSPM (R
> > 4.5.0)
> > gtable 0.3.6 2024-10-25 [1] RSPM (R
> > 4.5.0)
> > hms 1.1.3 2023-03-21 [1] RSPM (R
> > 4.5.0)
> > httr 1.4.7 2023-08-15 [1] RSPM (R
> > 4.5.0)
> > httr2 1.2.1 2025-07-22 [1] RSPM (R
> > 4.5.0)
> > IRanges * 2.43.5 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > jsonlite 2.0.0 2025-03-27 [1] RSPM (R
> > 4.5.0)
> > KEGGREST 1.49.2 2025-10-10 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > lattice 0.22-7 2025-04-02 [2] CRAN (R
> > 4.5.1)
> > lifecycle 1.0.4 2023-11-07 [1] RSPM (R
> > 4.5.0)
> > magrittr 2.0.4 2025-09-12 [1] RSPM (R
> > 4.5.0)
> > Matrix 1.7-4 2025-08-28 [1] RSPM (R
> > 4.5.0)
> > MatrixGenerics 1.21.0 2025-04-15 [1]
> > Bioconductor 3.22 (R 4.5.0)
> > matrixStats 1.5.0 2025-01-07 [1] RSPM (R
> > 4.5.0)
> > memoise 2.0.1 2021-11-26 [1] RSPM (R
> > 4.5.0)
> > org.Hs.eg.db * 3.22.0 2025-10-11 [1]
> > Bioconductor
> > pillar 1.11.1 2025-09-17 [1] RSPM (R
> > 4.5.0)
> > pkgbuild 1.4.8 2025-05-26 [1] RSPM (R
> > 4.5.0)
> > pkgconfig 2.0.3 2019-09-22 [1] RSPM (R
> > 4.5.0)
> > pkgload 1.4.1 2025-09-23 [1] RSPM (R
> > 4.5.0)
> > plyr 1.8.9 2023-10-02 [1] RSPM (R
> > 4.5.0)
> > png 0.1-8 2022-11-29 [1] RSPM (R
> > 4.5.0)
> > purrr 1.1.0 2025-07-10 [1] RSPM (R
> > 4.5.0)
> > R6 2.6.1 2025-02-15 [1] RSPM (R
> > 4.5.0)
> > rappdirs 0.3.3 2021-01-31 [1] RSPM (R
> > 4.5.0)
> > RColorBrewer 1.1-3 2022-04-03 [1] RSPM (R
> > 4.5.0)
> > Rcpp 1.1.0 2025-07-02 [1] RSPM (R
> > 4.5.0)
> > RCurl 1.98-1.17 2025-03-22 [1] RSPM (R
> > 4.5.0)
> > readr 2.1.5 2024-01-10 [1] RSPM (R
> > 4.5.0)
> > regioneR 1.41.3 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > remotes 2.5.0 2024-03-17 [1] RSPM (R
> > 4.5.0)
> > reshape2 1.4.4 2020-04-09 [1] RSPM (R
> > 4.5.0)
> > restfulr 0.0.16 2025-06-27 [1] RSPM (R
> > 4.5.1)
> > rjson 0.2.23 2024-09-16 [1] RSPM (R
> > 4.5.0)
> > rlang 1.1.6 2025-04-11 [1] RSPM (R
> > 4.5.0)
> > rprojroot 2.1.1 2025-08-26 [1] RSPM (R
> > 4.5.0)
> > Rsamtools 2.25.3 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > RSQLite 2.4.3 2025-08-20 [1] RSPM (R
> > 4.5.0)
> > rstudioapi 0.17.1 2024-10-22 [1] RSPM (R
> > 4.5.0)
> > rtracklayer * 1.69.1 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > S4Arrays 1.9.1 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > S4Vectors * 0.47.4 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > S7 0.2.0 2024-11-07 [1] RSPM (R
> > 4.5.0)
> > scales 1.4.0 2025-04-24 [1] RSPM (R
> > 4.5.0)
> > Seqinfo * 0.99.2 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > sessioninfo 1.2.3 2025-02-05 [1] RSPM (R
> > 4.5.0)
> > SparseArray 1.9.1 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > stringi 1.8.7 2025-03-27 [1] RSPM (R
> > 4.5.0)
> > stringr 1.5.2 2025-09-08 [1] RSPM (R
> > 4.5.0)
> > SummarizedExperiment 1.39.2 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > testthat * 3.2.3 2025-01-13 [1] RSPM (R
> > 4.5.0)
> > tibble 3.3.0 2025-06-08 [1] RSPM (R
> > 4.5.0)
> > tidyselect 1.2.1 2024-03-11 [1] RSPM (R
> > 4.5.0)
> > TxDb.Hsapiens.UCSC.hg19.knownGene * 3.22.0 2025-10-11 [1]
> > Bioconductor
> > tzdb 0.5.0 2025-03-15 [1] RSPM (R
> > 4.5.0)
> > UCSC.utils 1.5.0 2025-04-17 [1]
> > Bioconductor 3.22 (R 4.5.0)
> > usethis 3.2.1 2025-09-06 [1] RSPM (R
> > 4.5.0)
> > vctrs 0.6.5 2023-12-01 [1] RSPM (R
> > 4.5.0)
> > withr 3.0.2 2024-10-28 [1] RSPM (R
> > 4.5.0)
> > XML 3.99-0.19 2025-08-22 [1] RSPM (R
> > 4.5.0)
> > XVector 0.49.1 2025-10-07 [1]
> > Bioconductor 3.22 (R 4.5.1)
> > yaml 2.3.10 2024-07-26 [1] RSPM (R
> > 4.5.0)
> >
> > Thanks!
> >
> > --------------------
> > Raymond Cavalcante, PhD
> > Bioinformatics Analyst
> > Epigenomics Core and Bioinformatics Core
> > Biomedical Research Core Facilities
> > University of Michigan Medical School
> >
> > [email protected]
> > [email protected]
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > [email protected] mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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