I am running trinity on 4 data sets (2 left reads, 2 right reads) and I want it to be compiled into one assembled transcriptome. Just be to be sure, I should be selecting multiple data sets, selecting my trimmed files, and then running it on those? Why does it parse it out into 4 jobs when doing this and not have one final job to compile them? Does trinity through galaxy do that automatically at the end?
Any help would be much appreciated.