Question: the formula which calculate the rate of heterozygosity in kmer analysis
0
gravatar for 70910595
3.2 years ago by
709105950
709105950 wrote:

I want to calculate the rate of heterozygosity in kmer analysis。 I tried to use some software like BBMAP ,genomecope,gce.. But the results were not satisfactory。。 So,I want to know how could i calculate the rate of heterozygosity by myself。

Thank you for your help!

sequencing next-gen genome • 1.7k views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 3.2 years ago by 709105950
1
gravatar for Brian Bushnell
3.0 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

You can calculate the het rate of a diploid, approximately, like this:

Where K is the kmer length, A is the number of unique kmers in the first (1-copy) peak and B is the number of unique kmers in the second (2-copy) peak, and G is the haploid genome size:

hetRate=(A/K)/G

The genome size can be approximated by:

G=A/2+B

You can add the first repeat peak (4-copy) into the genome size with an extra term "+2*C", and so forth for higher copy peaks, but that typically doesn't have much effect.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Brian Bushnell16k

i just want to make sure, K is k-mer size?

ADD REPLYlink written 3.0 years ago by fgajardoe0

Yes, that's correct. I'll edit my answer.

ADD REPLYlink written 3.0 years ago by Brian Bushnell16k
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