[Bioc-devel] Masked version of BSgenome.Hsapiens.NCBI.GRCh38?

Hervé Pagès hpages at fredhutch.org
Mon Feb 9 08:23:26 CET 2015

Hi Ulrich,

I was not sure about how much demand there is for the masked BSgenome
packages in general so I was just waiting for someone to ask. Note that
the masks are typically generated from data available at UCSC so it
sounds that it's time to make BSgenome.Hsapiens.NCBI.hg38 and
BSgenome.Hsapiens.NCBI.hg38.masked available.

I'll prepare the 2 packages in the next couple of weeks and post back
here when they are ready for download.


On 02/06/2015 06:13 AM, Ulrich Bodenhofer wrote:
> Hi,
> The latest human genome build GRCh38 has been around in Bioconductor for
> some while (package BSgenome.Hsapiens.NCBI.GRCh38). As far as I can
> tell, however, there is currently no package that provides easy access
> to masked/unmasked regions in the genome (like there is a .masked
> version that wraps BSgenome objects into MaskedBSgenome objects for many
> other genomes, e.g. there is BSgenome.Hsapiens.UCSC.hg19.masked for
> hg19). Here is my question: does anybody have plans to include  a
> package BSgenome.Hsapiens.NCBI.GRCh38.masked (or under a different name)
> into Bioconductor 3.1? At least I could not find anything in the current
> development branch.
> Thanks and best regards,
> Ulrich
> ------------------------------------------------------------------------
> *Dr. Ulrich Bodenhofer*
> Associate Professor
> Institute of Bioinformatics
> *Johannes Kepler University*
> Altenberger Str. 69
> 4040 Linz, Austria
> Tel. +43 732 2468 4526
> Fax +43 732 2468 4539
> bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at>
> http://www.bioinf.jku.at/ <http://www.bioinf.jku.at>
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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