I have read that 30-50M reads mapped per sample are the general optimal number of reads mapped needed to do a DE expression analysis for mRNA-Seq. What would be the minimum for TOTAL RNA-Seq? Is it a lot more?
As a rough estimate: RNA is for 95% rRNA. If you are not depleting these in your TOTAL RNA-seq, and want to get the same number of reads on your 'interesting' mRNA then you can multiply that number of reads by 20.
As mentioned by WouterDeCoster 95% of cellular RNA is rRNA - therefore RNA library preperation always either do:
to enrich for the RNA of interest.
This is build into the library preparation protocols so you don't need to think about it. You just tell the sequencing center which one you want (if you don't say anything I would guess 95% would do poly-A selection).
Please note that often rRNA depletion is refereed to as total-RNA.
On the topic of number reads
On the topic of number reads I have 3 comments:
To do a gene differential expression analysis you need 5-10e6 reads
The number of independent biological replicates is the major determining factor in the power you have - you need at least 3 replicates in each condition!
If you want to do a transcript level analysis, enabling analysis of amongst other isoform switches, you need to to sequence deeper - 30-50e6 paried-end reads.
You can find more information about good practices in RNA-seq analysis here. Analysis of isoform switches - such as the analysis presented here can be done with my R-package IsoformSwitchAnalyzeR.