liftover
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Christina Akirtava
Oct 18, 2021, 5:31:47 PM10/18/21
to gen...@soe.ucsc.edu
To Whom It May Concern,
I have seen conflicting answers on google groups etc.
Best,
Christina
Christina Akirtava
PhD Candidate
McManus Lab
Department of Biological Sciences
Carnegie Mellon University
Pittsburgh PA
Luis Nassar
Oct 19, 2021, 2:42:56 PM10/19/21
to Christina Akirtava, UCSC Genome Browser Discussion List
Hello, Christina.
Thank you for your interest in the Genome Browser.
As you probably know, liftOver attempts to convert coordinates from one genome to another. It does so by using a chain file, which contains a best attempt to find homologous regions between the desired assemblies.
The more closely related the species the more successful the lift is.
Building these files between the same species (but different assemblies) allows one to use the most conservative settings. Meaning the specificity, or accuracy of the lift, should be higher. As that relationship widens, to say mouse and human, those parameters must be loosened. However, they are still mammalian genomes and fairly closely related compared to other vertebrates or say fish.
We offer chain files to liftOver between most all of our genome assemblies and human, including mouse to and from human. These can be found on our download server (https://hgdownload.soe.ucsc.edu/downloads.html). For example, here is the directory with all the mm39 assembly chain files (including human): https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/
While we cannot offer scientific advice and a definitive answer as to the fidelity of these lifts, we can share that we regularly use them ourselves. The lift is also highly dependent on the specific region of interest, as there are some highly conserved regions which match with very high confidence between mouse and human, just as there are some very divergent regions.
If you have some specific example regions or lifts you are looking to accomplish, we may be able to offer more information.
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Lou Nassar
UCSC Genomics Institute
Thank you for your interest in the Genome Browser.
As you probably know, liftOver attempts to convert coordinates from one genome to another. It does so by using a chain file, which contains a best attempt to find homologous regions between the desired assemblies.
The more closely related the species the more successful the lift is.
Building these files between the same species (but different assemblies) allows one to use the most conservative settings. Meaning the specificity, or accuracy of the lift, should be higher. As that relationship widens, to say mouse and human, those parameters must be loosened. However, they are still mammalian genomes and fairly closely related compared to other vertebrates or say fish.
We offer chain files to liftOver between most all of our genome assemblies and human, including mouse to and from human. These can be found on our download server (https://hgdownload.soe.ucsc.edu/downloads.html). For example, here is the directory with all the mm39 assembly chain files (including human): https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/
While we cannot offer scientific advice and a definitive answer as to the fidelity of these lifts, we can share that we regularly use them ourselves. The lift is also highly dependent on the specific region of interest, as there are some highly conserved regions which match with very high confidence between mouse and human, just as there are some very divergent regions.
If you have some specific example regions or lifts you are looking to accomplish, we may be able to offer more information.
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Lou Nassar
UCSC Genomics Institute
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