Question: Reasons why genome coordinates may not have a relative between reference genome assemblies
0
gravatar for Atu
5.0 years ago by
Atu0
Spain
Atu0 wrote:

I was wondering why might it be that a given coordinate in say, hg19, may not map to any coordinate in hg38. I have observed that, and I would like to know which are the reasons, conceptually,  that may cause the loss of a given coordinate when a new assembly is built. Also, and I guess related to this, I wonder why might a several coordinates from an assembly collapse into a single one in a different one.

alignment sequence assembly • 1.2k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Atu0
1
gravatar for harold.smith.tarheel
5.0 years ago by
United States
harold.smith.tarheel4.6k wrote:

The simplest explanation is that the one reference contains more assembled sequence (i.e., is larger) than the other, so the coordinate does not exist in the smaller reference. Similarly, a larger interval of multiple coordinates can collapse into a single coordinate in the smaller reference (or repetitive regions in the larger one may have been represented only once in the smaller assembly).

ADD COMMENTlink written 5.0 years ago by harold.smith.tarheel4.6k
0
gravatar for Atu
5.0 years ago by
Atu0
Spain
Atu0 wrote:

Thanks for your answer. As I read it I realize my question was not detailed enough. As the reason you have explained for the case where multiple coordinates may collapse, I meant to ask about biological reasons that may explain the discrepancies mentioned in my question. Thanks!

ADD COMMENTlink written 5.0 years ago by Atu0
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