HI,
You are right hg19 seems to be ok. But I am using hg18.
http://www.genome.ucsc.edu/cgi-bin/hgTables
Schema for Segmental Dups - Duplications of >1000 Bases of Non-RepeatMasked
Sequence
Database: hg18 Primary Table: genomicSuperDups
This is a sample I downloaded for chr2 locus and with only first 10 columns,
and I am using 'all fields from selected table' as 'output format'
#bin chrom chromStart chromEnd name score strand
otherChrom otherStart otherEnd otherSize
1310 chr2 95113102 95117052 chr5:126503096 15776 +
chr5 126503096 126506448 180857866
1313 chr2 95428891 95443771 chr2:96036782 205673 +
chr2 96036782 96052481 242951149
1313 chr2 95428896 95443771 chr2:97111880 205214 -
chr2 97111880 97127588 242951149
1313 chr2 95443771 95526464 chr2:95609272 1748861 -
chr2 95609272 95691902 242951149
As you can see the 'otherSize' != 'otherEnd' - 'otherStart'
Thanks
Sri.
Dr. Srirangan Sampath Ph.D.,
ABMG Clinical Cytogenetics Fellow
Medical Genetics Laboratories
Department of Molecular & Human Genetics
John P. McGovern Campus NABS-O250
Baylor College of Medicine,
Houston, TX-77021
Cell: 504-390-5512
________________________________________
From: Katrina Learned [[email protected]]
Sent: Friday, July 22, 2011 8:20 PM
To: Sampath, Srirangan
Cc: [email protected]
Subject: Re: [Genome] segmental duplications
Hi Srirangan,
Which assembly are you using? I just double checked this table on hg19
and the values in the fields you mention correspond with each other and
the browser. Can you please provide an example of one that isn't correct?
Thank you,
Katrina Learned
UCSC Genome Bioinformatics Group
Sampath, Srirangan wrote, On 07/21/11 20:55:
> Your outputs from table browser for segmental dups, the 'othersize' does not
> reflect 'otherEnd-otherStart'? Why is that? Even your 'Sample Rows' section
> this can be seen.
>
> Thanks
> Sri.
>
> Dr. Srirangan Sampath Ph.D.,
> ABMG Clinical Cytogenetics Fellow
> Medical Genetics Laboratories
> Department of Molecular& Human Genetics
> John P. McGovern Campus NABS-O250
> Baylor College of Medicine,
> Houston, TX-77021
> Cell: 504-390-5512
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
