[ensembl-dev] UTR extension for array mapping

[Nathan Johnson]

Hi Gavin

Setting the -utr_multiplier to 0 and omitting any other utr extension params will just use the transcript model i.e annotated UTRs. The reason why you are not getting any mappings is unclear to me at the moment as I don't really know anything about the array model you are mapping, but it maybe because the ensembl UTR annotations are conservative with repect the the transcript model which were use to design the probe/set.  This is exactly why we define UTR extension parameters. More details can be found here:

http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html

To set the 'Ensembl' defaults automatically you need to set -calculate_utrs -utr_multiplier 1

Nath


On 7 Dec 2010, at 12:43, Oliver, Gavin wrote:

> Hi,
>  
> They looked straightforward enough but I have managed to confuse myself with the UTR extensions in the EFG array mapping environment.
>  
> Basically I only want to map to a UTR if I can actually see it in the genome browser.
>  
> What settings should I use?
>  
> I tried setting all extensions to 0 but this resulted in zero annotation.
>  
> Best,
>  
> Gavin
>  
>  
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Nathan Johnson
Scientific Programmer
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
Email: njohnson at ebi.ac.uk
TelNo: (+44)1223 492629





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