[Genome] Syntenic Alignments

[J.J. Emerson]

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