How to derive sequence of novel transcript identified by Cufflinks

Question

[CY]

I am new to transcript level analysis using RNA-Seq. The goal is to retrieve sequence of newly identified transcript from RNA-Seq data. We just finished runing Cufflinks and seems like that a number of putative novel transcripts were generated. What do I have to do to further retrieve the sequence of novel transcript? Or at least recognize the exons included in novel transcripts? Thanks

[lieven.sterck]

do you have a reference transcriptome/genome at your disposal?

[CY]

Yes, it is reference guided.

[lieven.sterck]

in that case you can align your reads to the reference and then subtract all the ones that align to known genes and the leftover are the novel ones.

or is this not what you're asking for?