Liftover reference
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John Adams
Aug 16, 2016, 11:40:31 AM8/16/16
to gen...@soe.ucsc.edu
Hi,
- Please let me know the correct reference to use while citing liftOver utility.
- Does liftOver provide a 1:1 mapping between two genomes when run with the default settings? Which settings should be used to get 1:1 matches (discard multiple hits)?
Cath Tyner
Aug 17, 2016, 2:08:42 PM8/17/16
to John Adams, UCSC Genome Browser Public Help Forum
Hello Joh,
Thank you for your interest in the liftOver utility.
The NAR 2006 database issue mentions liftOver as a new feature in the browser:
Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H,
Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen
JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW,
Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS,
Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2006. Nucleic
Acids Res. 2006 Jan 1;34(Database issue):D590-8
If you ever have questions about what a Kent utility does, you can run the command with no arguments on the command line:
$ liftOver
This will print a usage message explaining what the program does and its various arguments and options. Note that liftOver was designed to work best between two different assemblies of the same species, not across species. Unfortunately, there is no exact answer for your question regarding 1:1 mapping. You can try adding in a -minChain or -minSize length for either the query or the target to see which works best for you to reduce the unwanted noise from short or non-specific matches. Or, run a few cycles, starting out strict, then making the parameters more permissive with the unMapped set based on the failure reason.The liftOver utility is just a tool. Experimenting with parameters and then evaluating the results from a scientific perspective is the recommended analyses path. LiftOver runs fairly quickly, so the best way to determine optimal parameters is usually a test/analyze methodology. Each experiment can be different and some regions of the genome can differ from other regions depending on the presence of repetitive elements, the type of gene(s), the finished state of the assembly, etc.
Here is more
I also recommend searching our public archive of previously answered mailing list questions
For example
Please respond to this list if you have further questions!
* Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu
Thank you for your interest in the liftOver utility.
The NAR 2006 database issue mentions liftOver as a new feature in the browser:
Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H,
Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen
JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW,
Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS,
Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2006. Nucleic
Acids Res. 2006 Jan 1;34(Database issue):D590-8
If you ever have questions about what a Kent utility does, you can run the command with no arguments on the command line:
$ liftOver
This will print a usage message explaining what the program does and its various arguments and options. Note that liftOver was designed to work best between two different assemblies of the same species, not across species. Unfortunately, there is no exact answer for your question regarding 1:1 mapping. You can try adding in a -minChain or -minSize length for either the query or the target to see which works best for you to reduce the unwanted noise from short or non-specific matches. Or, run a few cycles, starting out strict, then making the parameters more permissive with the unMapped set based on the failure reason.The liftOver utility is just a tool. Experimenting with parameters and then evaluating the results from a scientific perspective is the recommended analyses path. LiftOver runs fairly quickly, so the best way to determine optimal parameters is usually a test/analyze methodology. Each experiment can be different and some regions of the genome can differ from other regions depending on the presence of repetitive elements, the type of gene(s), the finished state of the assembly, etc.
Here is more
liftOver
information from our wiki.
I also recommend searching our public archive of previously answered mailing list questions
.
For example
Please respond to this list if you have further questions!
Thank you again for your inquiry and for using the UCSC Genome Browser.
Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:
* Confidential/private help: Email
genom...@soe.ucsc.eduUCSC Genome Browser Announcements List (email alerts for new data & software):
* Subscribe: Email genome-announce+subscribe@soe.ucsc.edu * Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu
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