[BioC] RinGO problem
Joern Toedling
toedling at ebi.ac.uk
Mon Jan 12 19:46:53 CET 2009
Hello,
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.
Regards,
Joern
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?
>
> exonerate-2.2.0-x86_64
>>
>> Can you also please tell me what the output of
>>
>> summary(allchranno$LENGTH)
>
>> summary(allchranno$LENGTH)
> 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
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