Trinity Output Filtering

Question

[Panos]

I have about 200,000 contigs in the Trinity output. I noticed that there are quite a few contigs having the same "comp" number. From what I've read so far this means that they are something like splice variants of the same gene.

So my question is how to filter Trinity output in order to remove at least some of this redundancy?

Answer 1

[Rm]

if you want to remove redundancy, try to cluster them based on similarity: you can try CD-HIT or blastclust or USEARCH