I have 3 (plant organism) paired-end biological replicates A161_1.fq 161_2.fq A162_1.fq A162_2.fq and A163_1.fq A163_2.fq. I did run Trinity transcriptome assembly on each paired sample, so now i got A161_trinity.fasta A162_trinity.fasta and A163_trinity.fasta. Now i need to do a GO analysis, and i wanted to ask 1) shouldn't i merge the output from trinity and how? or should i merge A161_1.fq with A162_1.fq and A163_1.fq (and the same with _2) and then run trinity again? i am trying to avoid running trinity again..! 2) i found transfuse online, in order for me to avoid running trinity again, but couldn't run it on my Mac. Any other solutions? And 3) for Go analysis should i run trinotate? or is there any other better/easier way?