I'm going to set up a RNA-seq experiment to characterize the transcriptome of different tissues of a species with a published genome in ncbi (but not a model species...). The aim is to characterize the tissue-specific transcriptome, evaluating eventual alternative splicing events. I'm going to make a 150 PE seq with a good coverage (at least 50M reads). The idea is to start from 3 pooled samples for each tissue in order to represent also variability occurring in different animals (what if a gene is not expressed in an individual for its specific conditions/characteristics?).
Going to the question: based on your experience, do you think that state-of-the-art transcriptome assembly softwares might have "problems" with reads coming from different animals? I'm thinking about polymorphisms... This should not be a problem, having a reference genome, isn't it?
Thank you in advance for your time and suggestions