[Genome] Question for a lower threshold for chain-score in the hg18 2006

[Robert Olinski]

Dear Hiram,

Thank you for your reply and I apologize for not being specific enough.
I was referring to human self-chains in hg18 March 2006, where a  
minimum score used by Blastz was 10,000 as compared to 2000 in hg17  
May 2004. In this way, some tracks displaying human self-chains from  
2004 release are simply not displayed in 2006 version. Would it be  
possible to human obtain self-chain track in hg18 with parameters from  
hg17? If not, I would very appreciate any suggestion from you on how  
to go about.

Big thanks!

Kind regards,
/Robert


Quoting Hiram Clawson <hiram at soe.ucsc.edu>:

> Good Evening Robert:
>
> Which set of chains exactly are you referring too ?  There are
> different minimum scores depending upon which chains they are.
> I'm curious which chains you mention that are in the May 2004
> assembly but not the March 2006 assembly ?  On the newest
> assemblies, we only keep the chains to the most recent version
> of the other organisms.  We do not keep the chains that existed
> before the minimum score filter was applied.  We would like to
> verify which chains you mention that were filtered at 10,000.
> Most chains should be at a filter of 5,000 or 3,000.
>
>
> You can fetch the chain files directly from the FTP server
> directory:
>
> ftp://hgdownload.cse.ucsc.edu/apache/htdocs/goldenPath/hg18/
> Note the directory names there beginning with vs
> in the form of vs<otherDb> for example:
> ftp://hgdownload.cse.ucsc.edu/apache/htdocs/goldenPath/vsMm9/
> for the Mouse assembly.  The file in that directory
> hg18.mm9.all.chain.gz contains all the chains.
>
> But these are after the minimum score filter has been
> applied.  Note also the README.txt files in each of
> these directories.  They should contain the minimum
> score filters used in the alignment, for example Mm9-Hg18
> was 3,000
>
>
> --Hiram
>
>
> Robert Olinski wrote:
>> Dear Madam or Sir at UCSC,
>>
>> 1) We have a problem with the human chains from the UCSC Genome    
>> Browser May 2006 hg18. According to the following information   
>> ?Chains  scoring below a minimum score of 10,000 were discarded?,   
>> the specified high threshold discarded relevant to us information   
>> for conserved  repetitive sequences in mammals that was present in   
>> 2004 release.  Therefore, we would like to know how (and whether)   
>> we could obtain all human chains with a lower threshold (possibly   
>> the ones used in the  2004 release of the human genome data) for   
>> 2006-human genome data. The May 2006 release contains many more   
>> species of interest that we want  to keep for PhastCons scores, but  
>>  some human chains from 2004 release  are simply not at all   
>> displayed in 2006 hg18 genome browser version.
>>
>> 2) How is it possible to download at once all chains displayed in   
>> the  genome browser window? Should we use the Table Browser for   
>> this  purpose? If so, does the following format would be acceptable  
>>  to  simply copy and paste into the table browser to get the   
>> sequence for  the given chain e.g
>> chain 13475906 chr1 247249719 + 120974 741471 chr1 247249719 +    
>> 220708072 222295432 494
>> or should we skip all coordinates and paste only numbers separated   
>> by a space?
>> Thanks a lot for help and for all answers!
>>
>> With best regards from Japan,
>> 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
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>