[Genome] question about STS on chr1_random

[Archana Thakkapallayil]

Hello Anyuan,

Please note this from our FAQ on the chrN_random chromosomes:
http://genome.ucsc.edu/FAQ/FAQdownloads#download10

"Starting with the April 2003 human assembly, these tables also include 
data for sequence that is not in a finished state, but whose location in 
the chromosome is known, in addition to the unordered sequence. Because 
this sequence is not quite finished, it could not be included in the 
main "finished" ordered and oriented section of the chromosome.

Also, in a very few cases in the April 2003 assembly, the random files 
contain data related to sequence for alternative haplotypes. This is 
present primarily in chr6, where we have included two alternative 
versions of the MHC region in chr6_random. There are a few clones in 
other chromosomes that also correspond to a different haplotype. Because 
the primary reference sequence can only display a single haplotype, 
these alternatives were included in random files. In subsequent 
assemblies, these regions have been moved into separate files (e.g. 
chr6_hla_hap1)."

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

Regards,

Archana
UCSC Genome Bioinformatics Group

Anyuan Guio wrote:
> hi colleagues,
>     Thank you very much to provide the excellent data on UCSC genome 
> website.
>     Now I have a question about the STS marker.
>     In table ucsc_stsMap, there are many markers whose chromosome are 
> like these: chr1_random, chr2_random, chr5_h2_hap1, chr6_qbl_hap2 etc. 
>  From FAQ on your website, I know that STS location like chrN_random is 
> sequence that is known to be in a particular chromosome, but could not 
> be reliably ordered within the current sequence. STS location like 
> chr6_qbl_hap2 is sequence for alternative haplotypes.
>     However, for those STSs located on chr1_random or chr6_qbl_hap2 also 
> have chromosome start and end position in the table ucsc_stsMap. What is 
> this position? If this position is the physical position on chromosome, 
> its' location is clear and should not be marked as chr1_random. If not 
> the physical position on chromosome, what is it?
>     Thanks very much!
>
> Anyuan Guo
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>