Confusion about the approximate coverage of RNASeq data

Question

[noushin.farnoud]

Hi All,

I know the formula for theoretical read depth is not quite applicable for RNASeq data, as previously explained very well in this Biostars post: human transcriptome size

So my question is when "coverage per sample" is reported, such as in below, is it usually estimated based on the total size of the "genome" as the "target size"? Or is it based on other experiment-driven parameters for each facility?

(if I use genome size, I get numbers that are close to the reported sample coverage numbers).

https://genohub.com/shop-by-next-gen-sequencing-project/#query=1389c0b35376676553e7c7bbad214f39

I appreciate your feedback

nfarnoud

Answer 1

[Devon Ryan]

If you read the manufacturer specs link on the right side of that form, you'll see that they recommend to use the "minimum number of reads per sample" metric rather than "minimum coverage per sample". This is simply to avoid the ambiguity in meaning.