[Genome] about "hg18.panTro2.all.chain.gz"

[Kate Rosenbloom]

Hello Jun,

The hg18.panTro2.all.chain.gz file  in our
/goldenPath/hg18/vsPanTro2 downloads directory contains
all chimp alignment chains, not just the reciprocal best.
These are the same chains displayed and described in
the "Chimp Chain" track on our Mar. 2005 human genome
browser.

We have a preliminary set of reciprocal best chains that
have not yet been through our quality review process.
These can be accessed at:

http://hgwdev.cse.ucsc.edu/goldenPath/hg18/vsPanTro2/ 
hg18.panTro2.rbest.chain.gz

     Cheers,
	Kate
-----
Kate Rosenbloom
UCSC Genome Bioinformatics

On Oct 6, 2006, at 12:11 PM, Jun Wang wrote:

> Hello everyone,
> 	I am wondering whether the file "hg18.panTro2.all.chain.gz" is the
> chain file of reciprocal best hits between human and chimp genomes,
> or the file of just one-direction hits,e.g. from human to chimp.
> 	If it is not the chain file of reciprocal best hits, I am wondering
> whether you have generated it and where I can find it.
> 	btw, I did look at the chain file and found that there are many
> cases that the same query was aligned to different hits or several
> different queries were aligned to the same hit.
> 	Thanks a lot!
>
> Jun
> 	
> 	
>
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