[Genome] Accessing the right chained self alignment in hg18

[Brooke Rhead]

Hello Robert,

If you would like to find information on the hg18 chain with the ID 494, 
you can look in the hg18.hg18.all.chain file (available here: 
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsSelf/).  Note that the 
chain file format is different from the net format.  See a description 
of the chain format here:
http://genome.ucsc.edu/goldenPath/help/chain.html

Look for a line beginning with "chain" and ending with "494".  For example:

grep '^chain.* 494$' hg18.hg18.all.chain

chain 13475906 chr1 247249719 + 120974 741471 chr1 247249719 + 220708072 
222295432 494

I hope this answers your question.  If I have misunderstood what you are 
asking, please do not hesitate to write back to the mailing list address.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Robert Olinski wrote:
> Hello there at UCSC!
> 
> I have a problem with identification of the desired sequence using  
> chained self alignment option in the human Genome Browser. For  
> example, string
> "fill 159921 30 chr1 + 220755888 30 id 494 score 2387 ali 30 qOver 0  
> qFar 220060138 qDup 0 type syn tN 0 qN 0 tR 30 qR 30 tTrf 0 qTrf 0"
> that came from hg18.hg18.net finds many syntenic hits for chromosome 1  
> with the following IDs 318; 4716115, etc. I would like to know how can  
> I find directly self aligned segment with ID 494 as specified in the  
> provided string.
> Thank you very much for your answer!
> 
> With regards,
> /Robert
> 
> Robert P Olinski, M.Sc.,PhD
> Graduate School of Bioscience and Biotechnology
> Department of Biological Sciences
> Tokyo Institute of Technology
> 4259 Nagatsuta-cho, Midori-ku, Yokohama
> 226-8501 Japan
> phone:+81-45-924-5744
> fax: +81-45-924-5835
> email: Robert.Olinski at neuro.uu.se
> email 2: robertinuppsala at hotmail.com
> 
> 
> 
> 
> 
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