[ensembl-dev] Funcgen array mapping - Probeset with strange annotation result

[Oliver, Gavin]

Hi all, 

 

One of our users has pointed out a probeset (affy utr format) that seems
to be retrieving some unexpected annotation info via the FuncGen array
mapping environment.

 

The probeset annotates to ENSG00000140853  but only seems to return
probe features for four probes i.e. the end result says 4/11 probes
align.  However when I look at the alignment manually using Ensembl or
NCBI it looks like all probes align.  

 

To try and ensure that my scripts aren't doing anything funny, I set up
a quick test like this:

 

my @probes = @{$probeset->get_all_Probes};

 

        foreach my $probe (@probes) {

                my @probefeatures = @{$probe->get_all_ProbeFeatures()};

                foreach my $feature(@probefeatures) {

                        print $feature->probe_id."\n";

                }

        }

 

And sure enough only 4 probe IDs are returned.

 

The probes look like this:

 

>probe:ADXBRCv2a520413:BRRS.12588_at:1019:477;
Interrogation_Position=313; Antisense;

CCTGCCCTGGAAGTAATCTTGCTGT

>probe:ADXBRCv2a520413:BRRS.12588_at:852:123;
Interrogation_Position=324; Antisense;

AGTAATCTTGCTGTCCTGGAATCTC

>probe:ADXBRCv2a520413:BRRS.12588_at:665:993;
Interrogation_Position=329; Antisense;

TCTTGCTGTCCTGGAATCTCCTCGG

>probe:ADXBRCv2a520413:BRRS.12588_at:295:809;
Interrogation_Position=353; Antisense;

GGGATGAGGCAGCTGCCGAGCTGGC

>probe:ADXBRCv2a520413:BRRS.12588_at:921:949;
Interrogation_Position=383; Antisense;

TGCTGCCGAAGATGGGCCGGCTGAA

>probe:ADXBRCv2a520413:BRRS.12588_at:1130:813;
Interrogation_Position=478; Antisense;

GGGTCTAGCATCCAAGTCATCCGCC

>probe:ADXBRCv2a520413:BRRS.12588_at:411:539;
Interrogation_Position=485; Antisense;

GCATCCAAGTCATCCGCCTCTGGAA

>probe:ADXBRCv2a520413:BRRS.12588_at:94:315; Interrogation_Position=491;
Antisense;

AAGTCATCCGCCTCTGGAATAACCC

>probe:ADXBRCv2a520413:BRRS.12588_at:307:341;
Interrogation_Position=508; Antisense;

AATAACCCCATTCCCTGCGACATGG

>probe:ADXBRCv2a520413:BRRS.12588_at:553:511;
Interrogation_Position=524; Antisense;

GCGACATGGCCCAGCACCTGAAGAG

>probe:ADXBRCv2a520413:BRRS.12588_at:1099:419;
Interrogation_Position=567; Antisense;

CTTTGCCTTCTTTGACAACCAGCCC

 

 

Can anyone suggest what might be happening?

 

Best, 

 

Gavin

 


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