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

[Nathan Johnson]

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



On 2 Mar 2011, at 12:31, Oliver, Gavin wrote:

> Hi,
>  
> I have rerun my array annotations with v61.  Everything seemed fine until I looked at the log and saw that perhaps 2 probesets per array have actually mapped to a transcript.
> Can you think of something obvious that might have gone wrong here?  The log output is below.
>  
> Best,
>  
> Gavin
>  
>  
> (Nathan I’m posting here incase you didn’t receive my mail)
>  
>  
> ::      ::      Running on probe2transcript.pl on: ni-cr-svc-slv.phar-services.com   ::      :: - Mon Feb 21 09:01:02 2011
>  
> ::      Params are:     --species homo_sapiens --transcript_dbname homo_sapiens_core_61_37f --transcript_host ni-cr-svc-bs3 --transcript_port 3306 --transcript_user root --transcript_pass pass --xref_host ni-cr-svc-bs3 --xref_dbname homo_sapiens_funcgen_61_37f --xref_user root --xref_pass pass --unannotated_5_utr 0 --unannotated_3_utr 0 -annotated_5_prime_extend 0 -annotated_3_prime_extend 0 --threshold 0.000005 --mismatches 2 -vendor AFFY -format AFFY_UTR -arrays ADXOCv1a520630 ADXBRCv2a520413 ADXECv1a520743 ADXLCv1a520538 ADXCRCG2a520319 HG-U133_Plus_2 ADXPCv1a520642 -import_edb
> ::      No probe DB params specified, defaulting to xref params
>  
>  
> ::      ::      Checking existing Xrefs ::      ::
>  
> ::      You have specified -utr_multiplier and a -3|5_prime_extend, -3|5_prime_extend will override where appropriate
> ::      Setting 3 unannotated UTR length to 0
> ::      Setting 5 unannotated UTR length to 0
> ::      Identified 167074 transcripts for probe mapping
> ::      Allowed mismatches = 2
> ::      Caching arrays per ProbeSet - Mon Feb 21 09:01:21 2011
> ::      Performing overlap analysis. % Complete:
> ::      0 ::    1 ::    2 ::    3 ::    4 ::    5 ::    6 ::    7 ::    8 ::    9 ::    10 ::   11 ::   12 ::   13 ::   14 ::   15 ::   16 ::   17 ::   18 ::   19 ::   20 ::   21 ::   22 ::   23 ::   24 ::   25 ::   26 ::   27 ::   28 ::   29 ::   30 ::   31 ::   32 ::   33 ::   34 ::   35 ::   36 ::   37 ::   38 ::   39 ::   40 ::   41 ::   42 ::   43 ::   44 ::   45 ::   46 ::   47 ::   48 ::   49 ::   50 ::   51 ::   52 ::   53 ::   54 ::   55 ::   56 ::   57 ::   58 ::   59 ::   60 ::   61 ::   62 ::   63 ::   64 ::   65 ::   66 ::   67 ::   68 ::   69 ::   70 ::   71 ::   72 ::   73 ::   74 ::   75 ::   76 ::   77 ::   78 ::   79 ::   80 ::   81 ::   82 ::   83 ::   84 ::   85 ::   86 ::   87 ::   88 ::   89 ::   90 ::   91 ::   92 ::   93 ::   94 ::   95 ::   96 ::   97 ::   98 ::   99 ::
> ::      Failed to extend 1 transcripts
> ::      Seen 0 5 prime UTRs with and average length of 0
> ::      Seen 0 3 prime UTRs with and average length of 0
>  
>  
> ::      ::      Writing ADXOCv1a520630 ADXBRCv2a520413 ADXECv1a520743 ADXLCv1a520538 ADXCRCG2a520319 HG-U133_Plus_2 ADXPCv1a520642 Xrefs        ::      :: - Mon Feb 21 18:26:37 2011
>  
> ::      Logging probesets that don't map to any transcripts - Mon Feb 21 18:26:37 2011
> ::      Updating 0 promiscuous probesets - Mon Feb 21 18:40:28 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)
> ::      HG-U133_Plus_2 distinct ProbeSet xrefs mapped(total xrefs):     1/54675(4)
> ::      ADXPCv1a520642 distinct ProbeSet xrefs mapped(total xrefs):     2/121563(2)
> ::      Mapped 9/167074 transcripts  - Mon Feb 21 18:40:39 2011
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