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

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.

Cheers,
H.

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>
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