Formula For Converting Sequence To Physical Coverage

Question

[Dan]

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

[Ido Tamir]

maybe you miss n the number of reads?

[Dan]

n is implied by the coverage

Answer 1

[Istvan Albert]

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.

[Dan]

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?

[Istvan Albert]

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