A question in terms of definition
2
0
Entering edit mode
5 months ago
A ★ 3.9k

Hello

I am struggling with a concept

In this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5528935/, they speak about the proportions of the genome affected by copy‐number change. I have segmentation file so that I have end and start for the position of where copy number change has happened. If I do, End-start/the length of human genome (3Gb), does this give me the proportion?

CNV WGS Genome • 215 views
2
Entering edit mode
5 months ago

Hello again, all good? Yes, you could try that, i.e., subtract start from end (End - Start = Xbp), but be careful about CN segments that may already be overlapping.

For the genome size, I would obtain an official figure from the Genome Reference Consortium:

This will always be an estimate, because we have not, as yet, sequenced certain parts of the genome, Also, the true length of each genome will slightly differ between individuals, and even differ between cells within the same individual due to copy number alterations and other events.

Kevin

1
Entering edit mode
5 months ago
Qiongyi ▴ 110

You may also consider to use the human effective genome size (~2.9G) as your denominator.