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)