Question: Coverage Calculation
6
gravatar for Raygozak
6.7 years ago by
Raygozak1.3k
State College, PA, Penn State
Raygozak1.3k wrote:

HI, if i'm sending samples for sequencing at say 30X coverage of a given genome, what is the relation between the 30X,40X coverage metric and the minimum number of reads that i should expect to get back from the sequencing?

Thanks

next-gen coverage • 9.2k views
ADD COMMENTlink modified 12 weeks ago by Biostar ♦♦ 20 • written 6.7 years ago by Raygozak1.3k
9
gravatar for Irsan
6.7 years ago by
Irsan6.9k
Amsterdam
Irsan6.9k wrote:

Let's say the read length is 100 bps/read and the genome you are sequencing is 3.000.000.000 bps (= human =3 Gbs) and the average coverage is 30x (calculated after alignment). The minimum number of bases that you should have in your raw data is

3.000.000.000 * 30= 90.000.000.000 bases.

Given you have a read length of 100 bps you should have

90.000.000.000 / 100 = 900.000.000 reads = 450.000.000 read pairs (if you did paired end sequencing)

However, not all your raw reads will map to the reference genome so the number will even be bigger, 450.000.000 is an estimate of the minimum

also see technote from illumina

When you are particularly interested in optimizing coverage for exome seq you might find this information useful

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Irsan6.9k
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