seqlevelsStyle for chrY in Drosophila?
1
0
Entering edit mode
@lizingsimmons-6935
Last seen 10 months ago
Germany

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>
genomeinfodb dmel seqlevelsstyle • 614 views
ADD COMMENT
0
Entering edit mode
@danielvantwisk-13028
Last seen 15 months ago

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 COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 268 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6