[BioC] BiomaRt and extracting genomic sequence

[Rob Illingworth]

Hi Steffen

Thank you very much for your help that works perfectly.

I will keep checking to see if and when ensembl make the current build 
available for this.

kind regards

Rob Illingworth


steffen at stat.Berkeley.EDU wrote:
> 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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>>
>>
>>
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>>     

>
>
>
>   

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