how many reads are necessary for Ribo-Seq analysis

Question

[Assa Yeroslaviz]

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

[taufiqbge]

Does anyone have answer for this question? I am also struggling to find an answer. Thank you.

Answer 1

[lieven.sterck]

I have no experience using mouse or fly for this, but have you tried googling for relevant papers?

here are a few (for plant cases though):

• https://www.sciencedirect.com/science/article/pii/S1535947620323707
• https://academic.oup.com/jxb/article-abstract/71/18/5323/5847851?redirectedFrom=fulltext

not exactly for the species you're looking for but might give you some pointers nonetheless.