Hello UCSC team,
Thanks for all the help,
The standalone tools I needed are now giving me reasonable outputs, but I'm not
sure about the exact parameters to use for my specific needs in
the liftOver tool:
In many introns the levels of conservation of distantly related species are
very low, with only some island of conserved regions (not only exons).
Sometimes I wish to map coordinates of different species in regions that are
200-500bp from the nearest conserved regions. Accordingly, in such cases I do
not need the to find exact coordinate match, but I want the nearest match.
Maybe you can suggest how to use liftOver in such case
Avi
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