I am designing a differential gene expression experiment in a non-model animal without a reference genome and I need your expertise.
My experiment has 2 different conditions in 2 different locations and I will have 3 replicates per condition. It is also a time-scale experiment with 4 different time points. Total of samples = ((2x3)x2)x4 = 48 samples.
My initial idea was to multiplex 12 samples per ILMN HiSeq lane at 50PE.
Since I don't have a reference I have to generate my own de novo transcriptome and here is where I need your help. I don't know if 50PE is going to be enough to generate a good reference transcriptome and maybe is better to go for 100PE in at least 2 lanes to have a better coverage.
What do you think? Of course, I have budget restrictions so I cannot sequence my 32 samples at 100PE.
Thanks for your help!