I recently performed the de novo assembly of plant RNA-seq data using Velvet/Oases with the multiple k-mer approach (merging of several sub-assemblies). The assembled transcripts were annotated and filtered for redundancy using CD-HIT EST.
However, I still have a lot of different isoforms and I've been asked to confirm that these isoforms are real and not due to some assembly error. Of course, being de novo I don't have the genome sequence to compare to. I could still use the nucleotide sequence of a closely-related plant of the same family but I am afraid that the distant between the 2 plants is too far and would not really help validating my assembly.
How would you proceed in this case ?
Thank you for your answers.