Futher analysis on Trinity fasta output

Question

[Whoknows]

Hi friends,

I used Trinity assembler for de-novo assembly of a plant transcriptome based on same group protocol "De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity",

But output (trinity.fasta) includes ~150,000 sequences which seems to be very lot.

Several tools were made for further assembly and clustering like CAP3,TGCIL,CD-HIT .,

How can I do this, to obtain a normal number of unigenes (less than 80,000 or 90,000)??

What is the protocol for further assembly on trintiy sequence output file ??(Not downstream)

Thanks