When you combine samples for de-novo transcriptome assembly with Trinity, do you suggest limiting the number of reads for each sample? I had read one of Matthew MacManes' papers awhile back suggesting 40 million reads was a good number for Trinity assemblies of most metazoans.
However, I have 28 samples across 3 treatments that I want to use for DESeq and so, if I follow the advice at BioStars here, that's 28x40 million reads = 1.1 billion reads going into a Trinity assembler... This seems like a troublesome amount. How is it suggested to combine these samples in situations like this?