LiftOver between different species?

[Gemma-Zhang-326]

Dear Professor Wang,

I would like to express my appreciation for your invaluable contribution in developing the tool, which has significantly facilitated my research endeavors. While utilizing the tool, I have encountered a particular concern pertaining to the liftOver process. Specifically, I have observed that the liftOver operation exhibits a notably high success rate when performed between different assemblies within the same species. However, when applying liftOver to genomic data from distinct species, such as the comparison between Human (hs1) and Mouse (mm10), the success rate appears to decrease substantially.

In light of this observation, I am inquiring whether there are strategies or modifications that can be implemented to enhance the success rate of liftOver, particularly when it is employed for cross-species genomic comparisons. One potential suggestion is the introduction of a parameter, such as "Minimum ratio of bases that must remap," with a user-configurable value, e.g., 0.1. This parameter could potentially optimize the liftOver process when working across species boundaries.

I eagerly await your response and insights on this matter.

Sincerely,

Gemma