Transcript quantitation without a genome?

[MikeyG]

Hi all,
Does anybody know of a way to effectively quantitate/map short reads without a genome sequence? I'm working with an unsequenced organism, and have performed de novo sequencing/assembly, but the quant does not seem trivial without a genome to map to. Any advice here would be greatly appreciated.
Thanks!
Mikey

[petang]

The only option is to use the RPKM (reads counts per kb per million) for each assembled contig.