I am fairly new to the field of transcriptomics and am doing a de novo assembly using my data, and since rnaSPAdes is fairly new I decided to give it a shot, but since there is no publication on it yet, i decided to compare it with a Trinity assembly from the same sample. However, I do not know what is the way to go, but I was thinking using FastOrtho and CD-Hit to find how similar they are, maybe some metrics like average transcript length, N50, and so on. Any suggestions on how this should be approached?
Might be useful.
For the transcriptome assembly, functional evaluation is more important than other parameters, like N50. So, I suggest to do blastx of the assembly against the closely related species and see how many contigs get the best hit, and also how many full-length contigs exist within the assembly. Also, you can use DETONATE package that specifically developed for evaluation of de novo transcriptome assembly.
Hope this helps.