[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

Institute of Cell Biology
The University of Edinburgh
Michel Swann Building
Mayfield Road
TEL:+44(0)131 650 8695

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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