I'm looking to perform RNA-seq on pairs of cell lines to look at differential gene expression and wondering what I can get away with to lower costs. 2 questions:
1) How many reads would be a good starting point? Would 20M be a reasonable place to start? 2) I understand I should have at least 2 biological replicates per cell line. Is it ok to combine the tubes into 1? Or should they be run separately? 3) RIbo-depletion costs $200 more than poly-A enrichment. Is it better to go with ribodepletion since it encompasses non coding RNA or is it common to try polyA enrichment first and then go with noncoding RNA if nothing is found with polyA?
Thanks in advance!