[Genome] Syntenic Alignments

[Kayla Smith]

Dear J. J.,

We don't consistently include the _random chromosomes when making self 
chains.  We did for hg17 but not for hg18, because they did not add 
meaningful information and made the resulting data too large.

Thank you for pointing out the error in the Human/Chimp Net file. This 
file has been re generated:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsPanTro2/hg18.panTro2.syn.net.gz

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group


J.J. Emerson wrote:
> Hello,
> 
> I'm browsing the human genome downloads section (1) and looking at  
> the human/chimp pairwise alignments (2).  Specifically, I'm  
> interested in the "syntenic net" file (3).  Anyway, when I download  
> that file, I notice a few things.  The first is that, despite the  
> '.gz' extension, it isn't in fact g-zipped.  It is just plain text.   
> Second, if I grep for "net" in the file, I notice that there are only  
> entries for a few chromosomes, which I have listed below (4).
> 
> The first question I have is, why do the "random" chromosomes show up  
> as nets in species comparison files but not in the self comparison  
> file (5)?  The second question I have is, why is the syntenic net  
> alignment (3) incomplete and unzipped, but tagged as zipped?  Can  
> this file be properly generated and posted to the downloads section?
> 
> Thanks a lot!
> 
> Cheers,
> 
> J.J. Emerson
> 
> References in e-mail:
> 
> 1.  http://hgdownload.cse.ucsc.edu/downloads.html#human
> 
> 2.  http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsPanTro2/
> 
> 3.  http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsPanTro2/ 
> hg18.panTro2.syn.net.gz
> 
> 4. Results of «$ grep 'net' hg18.panTro2.syn.net.gz»:
> net chr1 247249719
> net chr10 135374737
> net chr10_random 113275
> net chr11 134452384
> net chr11_random 215294
> net chr12 132349534
> net chr13 114142980
> 
> 5. http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsSelf/ 
> hg18.hg18.net.gz
> 
> 
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