Reads map in Tophat, but Cufflinks doesn't find transcripts

[janec]

I'm trying to analyse some RNA-seq data for the first time. We are looking for novel non-coding transcripts that are expected to (mostly) be unspliced of low abundance.

With that in mind I've managed to set up Cufflinks so it accurately reports some of the known transcripts from our region of interest, but it fails to report transcripts for adjacent sites which also have reads mapping to them, sometimes at apparently higher coverage.

I've been running cufflinks with the parameters:
-F 0 -j 0 --min_intron_lgth 1 --min-frags-per-transfrags 1

Any input into this would be most welcome, as I would like to report back to my colleagues asap.