I have a question. I have 6 samples in which I want to do metatranscriptomic sequencing, but my question now is whether I should use MiSeq or HiSeq technologies. I know HiSeq would give me much more reads depth but I am concerned about reads length as well. I am working with Antarctic samples so the microbial community is quite simple, however the organisms I might encounter are also not very well described, so longer reads would possibly help me further up with the assembly.
Any thoughts or experience about this?