Entering edit mode
I'm trying to convert Drosophila seqinfo from UCSC to Ensembl style. However, using seqlevelsStyle to convert from UCSC to Ensembl style for dm6 does not give me what I expected - "chrY" is still "chrY" after the conversion whereas other chromosomes go from e.g. "chr2L" to "2L" (see below). Is this correct? Should it be "chrY" or just "Y" for the Ensembl-style chromosome names? Based on the Ensembl website I think it should be "Y".
library("BSgenome.Dmelanogaster.UCSC.dm6")
Dmel <- seqinfo(Dmelanogaster)
seqnames(Dmel)[1:7]
# [1] "chr2L" "chr2R" "chr3L" "chr3R" "chr4" "chrX" "chrY"
seqlevelsStyle(Dmel) <- "Ensembl"
seqnames(Dmel)[1:7]
# [1] "2L" "2R" "3L" "3R" "4" "X" "chrY"
sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.5
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.42.0 rtracklayer_1.34.2
[4] Biostrings_2.42.1 XVector_0.14.1 GenomicRanges_1.26.4
[7] GenomeInfoDb_1.10.3 IRanges_2.8.2 S4Vectors_0.12.2
[10] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] lattice_0.20-35 XML_3.98-1.7 Rsamtools_1.26.2 bitops_1.0-6 GenomicAlignments_1.10.1
[6] grid_3.3.3 zlibbioc_1.20.0 Matrix_1.2-10 BiocParallel_1.8.2 tools_3.3.3
[11] Biobase_2.34.0 RCurl_1.95-4.8 SummarizedExperiment_1.4.0<font face="sans-serif, Arial, Verdana, Trebuchet MS">
</font>
This is fixed in GenomeInfoDb 1.12.1. People running the current version of Bioconductor (i.e. BioC 3.5) can update their installation with
biocLite().It seems that the OP is running BioC 3.4, which is not current. Note that we don't provide fixes for old Bioconductor versions. "The fix" is to upgrade to the most current version i.e. to BioC 3.5 (requires R 3.4).
Cheers,
H.