Hi Sri, It turns out that the data contributor changed the contents of the "otherSize" column. For hg19, it is otherSize - otherEnd. For hg18, it contains the size of the chromosome listed in the "otherChrom" field. (In general, total chromosome size is useful for converting coordinates from one strand to the other, so it would be useful to have it in the table.)
The description of the otherSize column (http://genome.ucsc.edu/cgi-bin/hgTables?db=hg18&hgta_group=varRep&hgta_track=genomicSuperDups&hgta_table=genomicSuperDups&hgta_doSchema=describe+table+schema) matches the contents of the hg19 table, but is incorrect for the hg18 table. Thank you for pointing out the discrepancy! I have reported the bug to our engineers. -- Brooke Rhead UCSC Genome Bioinformatics Group On 07/23/11 10:37, Sampath, Srirangan wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
