84018a1d6515b75a60de04a61dd6f3f80be38580 brianlee Tue Jul 5 09:32:02 2022 -0700 Adding a link in hgTracksHelp.html, linked to from liftOver CGI, to a new anchor on FAQdownloads#liftOver that provides an example of running the command-line tool, refs #29698 diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html index 819bcbf..641f166 100755 --- src/hg/htdocs/FAQ/FAQdownloads.html +++ src/hg/htdocs/FAQ/FAQdownloads.html @@ -645,30 +645,31 @@ which is accessed from the View menu on the Genome Browser annotation tracks page, supports forward, reverse, and cross-species conversions, but does not accept batch input. The LiftOver tool, accessed via the Tools link on the Genome Browser home page, also supports forward, reverse, and cross-species conversions, as well as batch conversions.

If you wish to update a large number of coordinates to a different assembly and have access to a Linux platform, you may find it useful to try the command-line version of the LiftOver tool. The executable file for this utility can be downloaded here. LiftOver requires a pre-generated over.chain file as input, available for selected assemblies from the Downloads page. If the desired file is not available, send a request to the genome mailing list and we may be able to provide you with one.

Using liftOver

Here is an example on how to set up and run LiftOver from the command line:

Download the LiftOver program for your computer's operating system here
Change permissions on that file so that it can be executed
```
 chmod +x liftOver
```

Run the program with no arguments to see the usage statement

 ./liftOver

 liftOver - Move annotations from one assembly to another
 usage:
    liftOver oldFile map.chain newFile unMapped