[BioC] RinGO problem

Joern Toedling toedling at ebi.ac.uk
Tue Jan 13 15:06:01 CET 2009

Hi Jianping,

the problem turned indeed out to be a change in the Exonerate output
file format. Now match start coordinates can be higher than the end
coordinate if the match is on the minus strand, while previously in this
case the output file would only contain the indication that the reverse
complement of the query.
I have modified the utility Perl script "condenseExonerateOutput.pl"
accordingly, and the modified script will be in the new development
version of Ringo (>= 1.7.3) .
This new script should resolve your problem, please let me know if it
does not.

The entries in PROBE_ID are the unique identifiers of the probes on the
array and in the example data these were for probes designed on the
assembly mm5 of the mouse genome. It's no source of concern that your
probes have completely different identifiers.

Best regards,

Jianping Jin wrote:
> Hi Joern,
> 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.
> Jianping

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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