Hello Ian, Your first question sounds like you are desirous of performing an intersection between the alignments of the affy U133Plus2 array and the all_mrna track. You can use our Table Browser to perform intersections. The guide is here: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
If you were instead looking to perform some joins, I can tell you some identifiers upon which you could join. hg18.all_mrna.qName = hg18.gbCdnaInfo.acc hg18.kgXref.kgId = hg18.knownToU133Plus2.name In the table browser, you can click on the "describe table schema" button to find this type of information. Here is a FAQ on how searches are performed in the browser: http://genome.ucsc.edu/admin/hgFindSpecHowTo.html Finally, one resource you may find to be of interest is that in addition to our track of alignments of the consensus sequences of the affy U133 Plus2 array, affymetrix has their own version of these alignments, and it is available as a custom track. To see that data, you would have to use their netaffx tool, click on "IVT Expression" and then click on "UCSC Query". Select an array, and you will be taken to our website, with a custom track turned on from affymetrix. Please contact Todd Lower (lowe @soe.ucsc.edu) if you have questions about the archaea browser. I hope this addressed all of your questions. Please let us know if we can be of further assistance. Kayla Smith UCSC Genome Bioinformatics Group Ian Yi-Feng Chang wrote: > Dear Dr. Smith > Thank you so much for your reply. > Actually, I used knownToU133Plus2 table. > however, there are only 24259 distinct affy probe IDs can map to knownGene. > And about 14000 affy probes are mapped to all_mrna by using affyU133Plus2 > table to join all_mrna table on tName, tStart, tEnd. > Is this a right way to map affy id to all_mrna accession id? > > Actually, my question was, If I query a gene name like KRTAP7-1, ucsc > genome browser will report a mRNA id: > AB096962<http://genome.ucsc.edu/cgi-bin/hgTables?position=AB096962&hgsid=114435832> > Is UCSC genome browser using full-text search ?? > > BTW, Is UCSC have any plan to release bacterial ucsc genome browser ( > archaea.ucsc.edu) for download? > > Tanks again. > > ian > > On Thu, Oct 23, 2008 at 10:35 AM, Kayla Smith <[EMAIL PROTECTED]> wrote: > >> Ian, >> >> Try using our table hg18.knownToU133Plus2. >> >> I hope that's helpful to you. Please don't hesitate to write back if that >> isn't what your looking for or you require further assistance. >> >> Kayla Smith >> UCSC Genome Bioinformatics Group >> >> On Thu, 23 Oct 2008, Ian Yi-Feng Chang wrote: >> >> Dear All, >>> I've some gene names from affymetrix u133 plus 2 chip >>> by joining all_mrna and it related tables ( >>> >>> http://genome.ucsc.edu/cgi-bin/hgTables?db=hg18&hgta_group=rna&hgta_track=all_mrna&hgta_table=all_mrna&hgta_doSchema=describe+table+schema >>> ), >>> >>> some gene names are still missing. >>> However, by using table browser search tool it can report a mRNA record to >>> me ( >>> http://genome.ucsc.edu/cgi-bin/hgTables?position=KRTAP7-1&hgsid=114435832 >>> ). >>> Therefore, I would like to know, is there any extra table can help me to >>> query these non-canonical gene names? >>> >>> Thanks >>> >>> ian >>> _______________________________________________ >>> Genome maillist - [email protected] >>> http://www.soe.ucsc.edu/mailman/listinfo/genome >>> >>> > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
