How is determined the exact length of a gap on a genome assembly?

Question

[Atu]

Hi everyone,

I was wondering how is known orgiven the length of a gap in a genome assembly.

Thanks

[h.mon]

Sometimes the length it is not know, when it is, it may be inferred from paired end / mate pair insert size information (if whole genome shotgun sequencing is used) or from fosmid / cosmid / BAC size information. It may also be inferred by other methods (e.g. genetic maps and / or physical maps).

Do you have a specific assembly in mind, or is this a general question?

[Atu]

Hi.

Yes, I was thinking on the human reference. I guess it is a genome deeply studied and that there will be several information sources, but I don't know how do they determined the exact length in bp of a gap, or the exact length in bp of a chromosome. Thanks

Answer 1

[h.mon]

See this post for a previus discussion here on Biostars, look at Ashutosh Pandey's answer.

If you google for "human genome gaps" you will find a lot of interesting information both in academic papers and in blog posts. For example see this post, make sure to read the discussion on the comments.

[Atu]

Thanks for your answer!