Question: How Can I Calculate The Depth Of The Sequencing?
2
gravatar for Shirel Weiss
7.5 years ago by
Shirel Weiss20
Shirel Weiss20 wrote:

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

read next-gen sequencing • 15k views
ADD COMMENTlink modified 7.5 years ago by Damian Kao15k • written 7.5 years ago by Shirel Weiss20

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

ADD REPLYlink written 7.5 years ago by Alex Paciorkowski3.3k
10
gravatar for Damian Kao
7.5 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

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".

ADD COMMENTlink modified 7.5 years ago by Alastair Kerr5.2k • written 7.5 years ago by Damian Kao15k

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...

ADD REPLYlink written 7.5 years ago by ALchEmiXt1.9k

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...

ADD REPLYlink written 7.5 years ago by ALchEmiXt1.9k
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