Oases "Confidence" - What Does It Mean ?

Question

[Pasta]

Hi,

Does anyone know what the confidence values exactly mean in the transcripts.fa file produced by Oases ?

The documentation is very vague about it ....

I found a bit of information on the Net (see below), but it doesn't make sense since I have values of 0, 1 or >1

The confidence scores assigned by Oases are a heuristic measure that expresses the uniqueness of a transcript in a locus. In the case of loci with only one or two possible transcripts, they/it are assigned a confidence of 1. In the case of more complex loci, if a transcript of a locus shares the majority of the contigs associated with a locus than the Confidence of the transcript is high (close to 1), whereas a Confidence Score close to 0 indicates that only few of the contigs of a locus are part of the transcript.

Any help would be greatly appreciated.

Answer 1

[Istvan Albert]

There is some discussion on this here, and probably the best would be to post on the Oases user list:

http://listserver.ebi.ac.uk/pipermail/oases-users/2012-September/000275.html

... the confidence just means that the sequence uses the majority of the contigs in that locus, more or less meant to indicate the dominant isoform of splice variants ...

.

[Pasta]

Thank you for your suggestion ;)