sequencing depth/coverage

Avro1986 · 12-12-2012, 10:31 AM

Hi everyone!

I am currently looking at cDNA expression. However, I don't understand the concept of depth/coverage. Some people say that it is how many times a nucleotide is sequenced. I thought that the greater the depth, the bigger the sequenced cDNA...

Finally, assuming it is the former, if we say a coverage of 20x, do we mean that we have sequenced that nucleotide in 20 independent runs? Moreover, is each run made with a different sample?

Thank you for your help.

kwaraska · 12-12-2012, 11:37 AM

Average Coverage means that -on average-in a given set, the base is read that many times. So 20X average coverage means on average every base will be read 20x. In reality this means that some will be read fewer and some more.

There is no need for different runs or different library preps. It simply means if you need more coverage you must do additional sequencing.

The size of the DNA (or cDNA) being sequenced has nothing to do with coverage. It simply means you have to red more bases to reach an average of what you want.

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12-12-2012, 10:31 AM	#1
Avro1986 Member Location: Montreal Join Date: Dec 2012 Posts: 10	sequencing depth/coverage Hi everyone! I am currently looking at cDNA expression. However, I don't understand the concept of depth/coverage. Some people say that it is how many times a nucleotide is sequenced. I thought that the greater the depth, the bigger the sequenced cDNA... Finally, assuming it is the former, if we say a coverage of 20x, do we mean that we have sequenced that nucleotide in 20 independent runs? Moreover, is each run made with a different sample? Thank you for your help.

12-12-2012, 11:37 AM	#2
kwaraska Senior Member Location: Boston,MA Join Date: Nov 2008 Posts: 122	Average Coverage means that -on average-in a given set, the base is read that many times. So 20X average coverage means on average every base will be read 20x. In reality this means that some will be read fewer and some more. There is no need for different runs or different library preps. It simply means if you need more coverage you must do additional sequencing. The size of the DNA (or cDNA) being sequenced has nothing to do with coverage. It simply means you have to red more bases to reach an average of what you want.