[Bioc-devel] seqlevelsStyle: EnsDb integration with UCSC based annotations

Rainer Johannes Johannes.Rainer at eurac.edu
Tue Feb 2 08:50:35 CET 2016

Dear All!

Just wanted to let you know that I just pushed the last changes to the ensembldb package (version 1.3.14) that allow an easier integration with non-Ensembl based annotation. In detail, I’ve implemented the seqlevelsStyle and seqlevelsStyle<- method from the GenomeInfoDb and now it’s possible to change the seqlevel style of an EnsDb object to e.g. “UCSC” which allows to use seqnames like chr1, chrX in the filters to fetch data from the EnsDb. Also, the returned GRanges objects have then UCSC style chromosome names.

However, there’s a problem with seqnames for which no mapping is available (i.e. not primary chromosomes). For now I’ve fixed that with the global option ensembldb.seqnameNotFound that allows to handle what is returned in such cases.

I hope some of you might find that new methodology helpful.

cheers, jo

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