How Can I Calculate The Depth Of The Sequencing?

Question

[Shirel Weiss]

I did "my select" study, and I got how many reads for the exons I designed. I also have the mean base coverage. my boss want me to calculate the depth and I'm lost... What should do? I

[Alex Paciorkowski]

This is a good start toward answering your question: http://biostar.stackexchange.com/questions/638/what-is-the-sequencing-depth

Answer 1

[Damian Kao]

Your mean base coverage should be = (number of reads mapped to exons * average read length) / total length of all exons.

Depth of sequencing should be = (total number of reads * average read length) / total length of all the exons.

So mean base coverage is your "experimental depth" and depth of sequencing is the "theoretical depth".

[ALchEmiXt]

Beware! This only accounts when you have a descently distributed coverage as determined by mapping. The average doesn't tell that much probably...oh maybe depenidng on the question why you want to know. Otherwise lok at the coverage distribution eg using a sliding window approach...

[ALchEmiXt]

Beware! I think this certainly true when you have a descently distributed coverage as determined by mappingbut not with high and low coverage regions. In that case the average doesn't tell that much probably...oh maybe depenidng on the question why you want to know. Otherwise you could look at the coverage distribution eg using a sliding window approach...