[BioC] RinGO problem
jjin at email.unc.edu
Mon Jan 12 21:55:35 CET 2009
There are 6247 probes with LENGTH <= 0 (actually <= -50). The minus sign
may refer to the genome strain. I checked the demo data set which also
contains minus values for LENGTH.
The only difference I can tell is the format of PROBE_ID. In the demo file
it is something beginning with MM, e.g. MM5000P01479955, while in my file
it is something like 5313_0514_0052.
--On Monday, January 12, 2009 6:46 PM +0000 Joern Toedling
<toedling at ebi.ac.uk> wrote:
> well, the culprit(s) is/are the matches with a negative entry in LENGTH,
> as these are not supposed to happen. I am not sure how these came about,
> but it might have to do with changes in Exonerate (the scripts were
> written for Exonerate version 2.0.0). I shall investigate this further
> and get back to you. But for the moment, I am afraid you will have
> either to discard these lines with negative length matches before
> calling posToProbeAnno (how many are these?) or find a way to correct
> them in the Exonerate output file.
> Jianping Jin wrote:
>> Hi Joern,
>> Please see below,
>> --On Monday, January 12, 2009 5:44 PM +0000 Joern Toedling
>> <toedling at ebi.ac.uk> wrote:
>>> Hi Jianping,
>>> I am not completely sure what the source of the error is yet, so bear
>>> with me as I am trying to find out.
>>> First, something could be wrong with the merged Exonerate output file.
>>> Which version of Exonerate are you using?
>>> Can you also please tell me what the output of
>> Min. 1st Qu. Median Mean 3rd Qu. Max.
>> -72.00 50.00 50.00 50.13 51.00 75.00
> Joern Toedling
> EMBL - European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD
> United Kingdom
> Phone +44(0)1223 492566
> Email toedling at ebi.ac.uk
Jianping Jin Ph.D.
Center for Bioinformatics
Room 3133 Bioinformatics building
University of Chapel Hill
Chapel Hill, NC 27599
E-Mail: jjin at email.unc.edu
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