Oases "Confidence" - What Does It Mean ?
1
1
Entering edit mode
11.4 years ago
Pasta ★ 1.3k

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.

velvet rna-seq • 2.9k views
ADD COMMENT
1
Entering edit mode
11.4 years ago

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 ...

.

ADD COMMENT
0
Entering edit mode

Thank you for your suggestion ;)

ADD REPLY

Login before adding your answer.

Traffic: 2095 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6