[ensembl-dev] Almost no annotation with v61 EFG Array Mapping

[Oliver, Gavin]

Hi Nathan, 

 

I had already checked the probe2transcript output - lots of alignments
to introns and antisense.  Nothing that points to why this is happening
though.

 

The two tables tell me nothing more.

 

I should point out that I ran all the same arrays using v59 and v60 and
there were no problems like this.

 

Gavin

 

 

________________________________

From: Nathan Johnson [mailto:njohnson at ebi.ac.uk] 
Sent: 10 March 2011 13:49
To: Oliver, Gavin
Cc: dev
Subject: Re: [ensembl-dev] Almost no annotation with v61 EFG Array
Mapping

 

Gavin

 

To understand what these are, you need to look at them in the database.
Look at the unmapped_object table and the unmapped_reason table for more
details.

Either that, or look in the probe2transcript output, as described in the
array_mapping.txt documentation.

 

Nath

 

 

 

 

On 10 Mar 2011, at 13:34, Oliver, Gavin wrote:





Any ideas on this Nathan?  With so many unmapped objects does it suggest
some problem with the reference data i.e. my funcgen database?

 

 

 

________________________________

From: Oliver, Gavin 
Sent: 09 March 2011 08:26
To: 'Nathan Johnson'
Cc: dev
Subject: RE: [ensembl-dev] Almost no annotation with v61 EFG Array
Mapping

 

Hi Nathan, 

 

Most seem to be unmapped (see the stats below).

 

Monitor looks fine.

 

Any ideas?  Undoubtedly it will be something simple I'm overlooking!

 

 

::      Logging probesets that don't map to any transcripts - Tue Mar  8
17:25:20 2011

::      Updating 0 promiscuous probesets - Tue Mar  8 17:38:45 2011

::      UnmappedObjects loaded:                 598994

::      ADXBRCv2a520413 distinct ProbeSet xrefs mapped(total xrefs):
1/60856(1)

::      ADXOCv1a520630 distinct ProbeSet xrefs mapped(total xrefs):
4/120373(7)

::      ADXECv1a520743 distinct ProbeSet xrefs mapped(total xrefs):
4/111012(7)

::      ADXLCv1a520538 distinct ProbeSet xrefs mapped(total xrefs):
4/60416(10)

::      ADXCRCG2a520319 distinct ProbeSet xrefs mapped(total xrefs):
2/61528(2)

::      ADXPCv1a520642 distinct ProbeSet xrefs mapped(total xrefs):
2/121563(2)

::      HG-U133_Plus_2 distinct ProbeSet xrefs mapped(total xrefs):
1/54675(4)

::      Mapped 9/167074 transcripts  - Tue Mar  8 17:38:57 2011

 

________________________________

From: Nathan Johnson [mailto:njohnson at ebi.ac.uk] 
Sent: 03 March 2011 11:09
To: Oliver, Gavin
Cc: dev
Subject: Re: [ensembl-dev] Almost no annotation with v61 EFG Array
Mapping

 

Hi Gavin

 

Have you checked the unmapped objects? These should give you a clue.

 

Also, you might want to check the pipeline output  i.e. 'monitor' and
the ProbeAlign reports. This should show you see exactly what features
you are trying to xref.

 

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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