Question: Formula For Converting Sequence To Physical Coverage
0
gravatar for Dan
7.2 years ago by
Dan520
Cambridge
Dan520 wrote:

If I have reads of length x, inserrt size of y and genome size z, how do I convert from sequence to physical coverage?

sequencing • 4.3k views
ADD COMMENTlink modified 7.2 years ago by Istvan Albert ♦♦ 86k • written 7.2 years ago by Dan520
2

maybe you miss n the number of reads?

ADD REPLYlink written 7.2 years ago by Ido Tamir5.1k

n is implied by the coverage

ADD REPLYlink written 7.2 years ago by Dan520
1
gravatar for Istvan Albert
7.2 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

N = number of reads, L=length of each read, G=genome size

The "normal" definition of coverage would be C = N * L / G

Now if you want to extrapolate from that you could use the insert size for L but then you would need to also divide N by 2 as two reads form a pair. This would be more of a fragment coverage rather than actual base coverage.

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Istvan Albert ♦♦ 86k

Yes, that's what I call physical coverage. So I need to write two equations and solve to get the ratio? Is the ratio directly proportional to L1/L2?

ADD REPLYlink modified 7.2 years ago • written 7.2 years ago by Dan520

instead of read length use fragment length, though it is not clear from your description what you mean by insert size? how do you know that? If it is by alignment then note that it could be wrong, hence extrapolating from that to physical coverage may also be incorrect

ADD REPLYlink written 7.2 years ago by Istvan Albert ♦♦ 86k
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