I am studying RNA-Seq pipelines and would like some advice on how to deal with genes isoforms. Since we deal with sequencing of eucaryotes at the lab, such occurrence is very common. We use Trinity for de novo transcriptome assembly and we intend to use CD-HIT (cd-hit-est), at first, to cluster the isoforms. The questions are: the best time to perform this step is before or after the transcriptome assembly? Can CD-HIT be used as a preprocessing tool to remove duplicates/redundant reads after sequencing? Or is it best used to improve the assembly afterwards (as we are intending)?
If you know other approaches/tools to handle this situation, please let me know.
Thank you in advance! :)