[Genome] how scaffold-->chrUn?

[Ann Zweig]

Hello again, Xianjun,

	One of my colleagues has a suggestion for you.  You may be able to 
extract the information you want from either of these two database 
tables: gold or ctgPos.  You can use the Table Browser to query these 
tables, or you can download them from our download server.

	Alternatively, you could look in the AGP files we provide on our 
download server:  http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/

chromAgp.zip - Description of how the assembly was generated,
      unpacking to one file per chromosome.

contigAgp.zip - Description of how the assembly was generated
     from fragments at a contig layout level.


	I hope this information is helpful to you.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu




Ann Zweig wrote:
> Hello Xianjun,
> 
> 	I'm not sure I understand exactly what you are asking.  Are you saying 
> that you would like to know how to convert from scaffolds to chrUn?
> 
> 	In our browser, ChrUn contains clone contigs that can't be confidently 
> placed on a specific chromosome. For the chrN_random and chrUn_random 
> files, we essentially just concatenate together all the contigs into 
> short pseudo-chromosomes. The coordinates of these are fairly arbitrary, 
> although the relative positions of the coordinates are good within a contig.
> 
> 	If this does not answer your question, please don't hesitate to write 
> back to the list with more detailed information.
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> Please feel free to search the Genome mailing list archives by visiting 
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> 
> 
> 
> Xianjun Dong wrote:
>> hi, 
>>
>> How can you create chrUn by scaffolds? Is there a way to get the coordinate on chrUn for a region on some scaffold? i.e. scaffold212:12345-67890
>>
>> Thanks
>>
>> Xianjun
>>
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