Finding splice variants in de novo transcriptome data

[tboothby]

Hello,
I have recently finished assembling RNAseq data using Trinity. I am interested in finding an efficient way to identify splice variants.

All the tools I have come across do this by mapping short reads onto a reference genome (which I do not have).

Does anybody know a tool or can anyone think of a way to efficiently do this?

Cheers,
T

[pbluescript]

You essentially do have a reference transcriptome now. You can try mapping your short reads to your assembled transcripts.