[ensembl-dev] [SPAM] - Re: UTR extension for array mapping - Email found in subject

[Oliver, Gavin]

Thanks a lot Nathan!

 

I will give that a go now.

 

Best, 


Gavin

________________________________

From: Nathan Johnson [mailto:njohnson at ebi.ac.uk] 
Sent: 07 December 2010 13:13
To: Oliver, Gavin
Cc: dev at ensembl.org
Subject: [SPAM] - Re: [ensembl-dev] UTR extension for array mapping -
Email found in subject

 

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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