I thought 'getSequence' from the biomaRt package should allow you to
what you want. But, I can't seem to get it to work for genomic
ens <- useMart("ensembl","hsapiens_gene_ensembl")
Error in getSequence(chromosome = 1, start = 10000, end = 11000,
= "genomic", :
Please specify the type of sequence that needs to be retrieved when
using biomaRt in web service mode. Choose either gene_exon,
transcript_exon,transcript_exon_intron, gene_exon_intron, cdna,
3utr or 5utr
R version 2.10.0 (2009-10-26)
attached base packages:
 tools stats graphics grDevices datasets utils
other attached packages:
 biomaRt_2.2.0 Biobase_2.6.0
loaded via a namespace (and not attached):
 RCurl_1.2-1 XML_2.6-0
Johannes Waage wrote:
> Hi all,
> Is there a way to fetch genomic sequences via Bioconductor directly?
> galaxy, but I would like to automate)
> I tried rtracklayer and biomaRt - rtracklayer doesn't seem to have
> interface for fetching sequences, and biomaRt only seems to fetch
> from a subset of gene ID's, while I just to need to fetch sequence
> genomic range.
> fetchSequence(chr, strand, start, end) -> sequence
> Any suggestions?
> Thank you in advance!!
> Best regards,
> Uni. of Copenhagen
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