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Question: seqlevelsStyle for chrY in Drosophila?
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gravatar for liz.ingsimmons
6 months ago by
United Kingdom
liz.ingsimmons120 wrote:

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>
ADD COMMENTlink modified 6 months ago by daniel.vantwisk30 • written 6 months ago by liz.ingsimmons120
0
gravatar for daniel.vantwisk
6 months ago by
daniel.vantwisk30 wrote:

Thanks for identifying the bug!  It looks like the mapping tables in GenomeInfoDb need to be updated.  We'll post again once the issue is fixed.

ADD COMMENTlink written 6 months ago by daniel.vantwisk30

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.

ADD REPLYlink written 5 months ago by Hervé Pagès ♦♦ 13k
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