[BioC] BiomaRt and extracting genomic sequence

[steffen at stat.Berkeley.EDU]

Hi Rob,

This is currently not possible using biomaRt in web service mode.  However
the Ensembl team will probably make this available to us in the near
future.

If you're using the current release version of biomaRt (1.16.0) then you
should be able to get genomic sequences (unfortunately only from Ensembl
version 47) by:

>mart = useMart("ensembl_mart_47", dataset="hsapiens_gene_ensembl",
mysql=TRUE)
>seq = getSequence(chromosome = 20, start=20000, end = 20010, mart=mart)
> seq
  chromosome start   end    sequence
1         20 20000 20010 TGAGGTCTTAC


Note that this MySQL mode retrieval of genomic sequences will be replaced
by the default web service mode use of biomaRt.

Cheers,
Steffen

> 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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