Hi Kay, Because this track contains duplications, any sequence annotated as an item (row in the table) also has another location on the genome. So, each item has chromStart, chromEnd that refers to a location of that sequence. The OtherChrom, otherStart, and otherEnd fields provide the chromosome, start position and end position of the other location of that sequence. The "name" location is the name we've given to the item current location (but it is basically the chromosome and the start coordinate of the other location). That way, when you're looking at items in the browser, you'll be able to easily tell where its other location is.
I think it might be really helpful to see this track in the browser. I have created a session for you here: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Katrina&hgS_otherUserSessionName=SegDupExample The item displayed is in this location: chr5:171,221,300-171,223,711. However, its name (in the label area on the left of the image) is " chr21:31918136," which tells you that the other location of this duplicated sequence is on chromosome 21 starting at base 31,918,136. If you click on the item, you can get more specific details about this item (from the table) and about its second location; it also provides a link to the other location (click on the "Other Position" link). I think this should help you to better understand the table schema and sample data there. I hope this is helpful. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 9/9/11 1:08 PM, Kay Jaja wrote: > I have looked into the "View table schema" and I am still not clear > on how the different fields relate to each other. can you give an > example from the segDup data set and explain what it means. > > thanks, > > *From:* Katrina Learned <[email protected]> > *To:* Kay Jaja <[email protected]> > *Sent:* Friday, September 9, 2011 11:31 AM > *Subject:* Re: [Genome] question related to the downloads from the > UCSC database > > Hi Kay, > > Thank you for your question. To receive an answer in the timeliest > manner and so all our users can benefit from your question and its > answer, please resend your email to our mailing list: > [email protected] <mailto:[email protected]>. > > Thank you, > > Katrina Learned > UCSC Genome Bioinformatics Group > > On 9/9/11 11:13 AM, Kay Jaja wrote: >> thanks for your e-mail, I have looked into the "View table schema" >> and I am still not clear on how the different fields relate to each >> other. can you give an example from the segDup data set and explain >> what it means. >> >> thanks, >> >> *From:* Katrina Learned <[email protected]> >> <mailto:[email protected]> >> *To:* Kay Jaja <[email protected]> <mailto:[email protected]> >> *Cc:* "[email protected]" <mailto:[email protected]> >> <[email protected]> <mailto:[email protected]> >> *Sent:* Friday, September 9, 2011 9:02 AM >> *Subject:* Re: [Genome] question related to the downloads from the >> UCSC database >> >> Hi Kay, >> >> For more information about the track and table, please see the track >> description: >> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=genomicSuperDups >> <http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=genomicSuperDups> >> >> From here, click on "View table schema," and you will find a short >> description of each field of the table. >> >> Please contact the mail list ([email protected] >> <mailto:[email protected]>) again if you have any further questions. >> >> Katrina Learned >> UCSC Genome Bioinformatics Group >> >> >> On 9/8/11 6:19 PM, Kay Jaja wrote: >> > I have downloaded the list of segmental >> > duplications (hg18) using the following link >> > >> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/genomicSuperDups.txt.gz >> > from that file, you have chrom, >> > chromStart, chromEnd, which is the location of the segmental >> duplication on the >> > reference genome. In the fifth column there is a “name” field, How >> > is “name” field relate to chrom, chromStart, chromEnd? Also the fields >> > OtherChrom, otherStart, otherEnd. >> > Thanks, >> > _______________________________________________ >> > Genome maillist - [email protected] <mailto:[email protected]> >> > https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
