I'm using cufflinks denovo and cuffcompare to find un-annotated exons (in mouse as well as other genomes). When viewing the exons predicted by this pipeline in UCSC genome browser most line-up very well to my expression track, however a few do not.
My questions is this: When cufflinks denovo predicts an exon, does the output indicate any measure of confidence that indicates how certain cufflinks is of the exon's boundaries? That is, I'm looking for some measure of confidence of the exon's coordinates predicted by cufflinks.
Thank you
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