[BioC] BiomaRt and extracting genomic sequence
RS Illingworth
R.S.Illingworth at sms.ed.ac.uk
Mon Jan 26 22:05:21 CET 2009
Hello to the list
I have recently started mapping next generation sequencing data to the
human genome and would now like to map this to genes and other
annotated genomic features. Whilst I have found that I can map and
sort genes with the biomaRt package I have completely failed to
extract genome sequence using simple chromosome coordinates. I have
looked through the documentation for this package and have tried to
use the getSequence function but to no avail. The 'seqType' values all
seem to relate to gene associated sequences and 'type' has no obvious
value for genomic sequence and as such return an error msg. I think
there is probably a very straight forward solution which I am missing
and I would be very grateful if anyone could help.
Thanks for your assistance
kind regards
Rob Illingworth
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