[Genome] self chain, difference between versions

[Maximilian Haeussler]

Hi gurus,

I have the impression that hg16 showed many more self-chains in some
regions than hg18.  This is not true in general (table browser shows
600 MB versus 900 mb coverage) but for some regions that I'm
interested in. I'm wondering where that could come from?

Here is an example: Region chr4:109,636,597-109,636,813 on hg16 has
three paralogs, whereas its liftOvered-homolog on hg18 has none.
Similar for chr4:112,226,250-112,226,479 (20 paralogs found) on hg16
and chr4:111,986,879-111,987,108 on hg18 (0 paralogs found). According
to the track description, you haven't changed the blastz-parameters
since then... is it the updated repeatmasking that makes the results
change so much?  Or am I'm looking at the totally wrong track on Hg18?

(I couldn't easily compare makeHg16 and makeHg18 as they run different
shellscripts for blastz-ing/chaining)

And yes, thanks once again for your impressive efforts in answering
the questions on this mailing list!!

Max