Alignment percentage for De novo analysis

Question

[madhul27_sit]

Hi, I have a data of silkworm (some rare species) whose genome is not reported yet. Thus I am doing De novo RNA seq analysis of it. I have followed Trinity protocol and when I perform RSEM for abundance estimation, it is giving me 50, 46, 51, 44 , 47 and 57 percent overall alignment rate, respectively, for each sample. Ideally, above 70% overall alignment rate is considered best. So, Does that mean there is a problem with data or should I try some other method for alignment and abundance estimation?

I have two samples with 3 biological replicates each.

[h.mon]

By "followed the Trinity protocol", you mean you assembled the transcriptome with all the reads, then mapped each sample onto this reference transcriptome? What were the commands you used?