(B)LASTZ Parameters for Creating Liftover Chains for Mapping between Different Assemblies of the Same Species

[Irene Miriam Kaplow]

I am trying to create liftover chains for mapping between different
assemblies of the same species.  Which (B)LASTZ parameters should I use
for this?  Do I just use the default parameters?  Does this depend on
the species?  Thanks so much!

[Jairo Navarro Gonzalez]

Hello Irene,

Thank you for using the UCSC Genome Browser and your question about creating same species liftOver files.

When we create our liftOver files between different assemblies of the same species, we use BLAT to generate the alignments and not lastz. We have a Perl script that you can use to create the liftOver files and can be found on the following wiki page:

http://genomewiki.ucsc.edu/index.php/DoSameSpeciesLiftOver.pl

Unfortunately, it is beyond the scope of this mailing list to provide scientific advice such as the lastz parameters to use to generate your alignments between different species. We do have some examples for a human to other species alignments on the following wiki page:

http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl#lastz_parameter_file

If you still have questions specific to lastz parameters after reading our wiki pages, I would recommend contacting the lastz mailing list:

http://lists.bx.psu.edu/listinfo/lastz-users

I hope this is helpful and if you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genome Browser

Want to share the Browser with colleagues?
Host a workshop: https://bit.ly/ucscTraining

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/420a8ec5-31fc-9b69-937c-a0f3645ade78%40andrew.cmu.edu.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.