[BioC] RinGO problem

Joern Toedling toedling at ebi.ac.uk
Mon Jan 12 19:46:53 CET 2009


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?
> 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

More information about the Bioconductor mailing list