Could Cufflinks be used for calculating RNA read abundances only?

[hellsingwyk]

Dear all,

Since Cufflinks include the function of assembly and RNA scaffold abundance calculation, I would like to ask is it possible if I only use this tool for abundance calculation ?

I ask this question because I am doing RNA metagenomic research, so not all the RNA were came from human. And I would like to use MetaVelvet for assembly first.

So, is it possible to do that?