I have de novo RNAseq data (Illumina Hiseq) from multiple organs of a single animal. I have tried Velvet/Oases with multiples kmer against data from each organ, which finally yielded (as Oases -merge output) a transcript.fa file for each organ. Now I would like to make a whole reference transcriptome of this animal, how can I merge those transcripts obtained from multiple organs (to cut off those redundant part between them)? should I break down those transcripts.fa to kmer and reassemble them?
By the way, at the moment, which is the best suited tool for my purpose? Thank you in advance for your suggestion!