Using the normal N50 metric for transcriptome assemblies can be highly misleading, as transcriptomes do not strive to achieve long contig lengths and high N50, but instead one contig for each transcript. Furthermore, the most highly expressed transcripts do not necessarily constitute the longest ones and the majority of transcripts in a transcriptome assembly will normally have relatively low expression levels. Check out this discussion on biostars.
Is it true that N50 is not an important parameter for quality in Transcriptome Assembly?
The N50 values can often be exaggerated due to an assembly program generating too many transcript isoforms, especially for the longer transcripts. To mitigate this effect, Trinity assembler also compute the Nx values based on using only the single longest isoform per 'gene':
## Stats based on ONLY LONGEST ISOFORM per 'GENE':
Contig N10: 3685
Contig N20: 1718
Contig N30: 909
Contig N40: 588
Contig N50: 439
Go though this paper for methods to evaluate transcriptome assembly
My take is that even for genome assemblies, N50 should be taken with a pinch of salt, as it can mislead the assembly evaluation. If you want to learn more, check out this blog post
Why is N50 used as an assembly metric (and what's the deal with NG50)?