I am working on a project with collaborators in which one of our aim is to examine differential gene expression in humans across two time points. So is gene expression different at time 1 and time 2. We will be using RNA-sequencing and are getting some conflicting opinions from our "experts" as far as read depth.
Expert 1 says 2x50bp and everything they do with RNA is 2x50. And only use 2x100 if you are interested in increasing sensitivity for detecting snps and indels
Our sequencing core says 2x50bp is what "all their investigators using RNAseq use."
Expert 2 says 2x100bp and that essentially 2x50 is "old school"
We aren't sure which direction to go (or who is right!). We are not necessarily interested in detecting snps or indels, but our interest is purely identifying gene expression changes. Depending on which expert recommendation we go with drastically changes our budget. 2x100 doubles the cost of sequencing. So if we increase the costs we had planned for sequencing, that is a lot less samples/replicates we can sequence. We actually wouldn't be able to afford to sequence all of our collected samples, which seems like a waste! Our preference would be to stick with what we originally planned and budgeted for and 2/3 of our experts are telling us 2x50.