[BioC] [Fwd: [Genome-announce] Note on human mitochondrial sequence in hg19]

Hervé Pagès hpages at fhcrc.org
Thu Jul 30 03:42:41 CEST 2009

Hi BSgenome data package users,

I'm forwarding this important announcement that was sent today
to the Genome-announce mailing list (UCSC). The consequence of this
is that our BSgenome.Hsapiens.UCSC.hg19 package suffers from the
same problem, that is, the sequence for chrM is NOT the Revised
Cambridge Reference Sequence either. And, like the UCSC Genome people,
we won't update the chrM sequence so we remain consistent with the
UCSC genome browser.

If people really want us to support the updated GRCh37 assembly, then
we can still make a BSgenome.Hsapiens.GRC.GRCh37 package (wheere, if
I understand correctly, only the chrM sequence would differ from hg19).


Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319
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