it is a simple question, but seems to have no straight forward answer to. We are planning a ribo-seq experiment. I know from reading that many of the reads are being filtered out during the downstream analysis (rRNA, tRNA, duplications, etc.).This leaves a relatively small portion of the reads for downstream analysis.

For that reason i would like to know, if anyone has done this kind of experiments before and can recommand a numer/region of million reads needed to get enough reads at the end to be able to do a meaningful analysis

In our case we're talking about mouse and fruit fly as a reference genome.

thanks