Hi, Anton. It sounds like you're starting with RefSeq genes selected in the table browser. So, when you select output to "fields from primary and related tables" check the "rgdGene2ToRefSeq" table and click the "allow..." button. Now in the list will appear a table called "rgdGene2ToDescription". Check that one and click "allow...." again. You want the "value" field from that table.
If you have any additional questions, please reply to: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 7/16/12 12:44 AM, Anton Kratz wrote: > Dear UCSC team, > > [This is with respect to rat, rn4 assembly.] > > I could get a table with RefSeq ID, GeneSymbol and description of the > GeneSymbol using the instructions below. Thank you very much. > > I have a follow-up question regarding descriptions. I noticed that there > are at least two types of descriptions in the UCSC database. > > One is the description which I get using the method described below (from > gbCdnaInfo table). > > The other is at least linked to RGD. > > For example the GeneSybol Calb1 via RefSeq has "Description: Rattus > norvegicus calbindin 1 (Calb1), mRNA." acording to gbCdnaInfo. Let's call > this description1. > > When checking Calb1 via RGD the description is "Description: binds calcium; > activity is vitamin D dependent". Let's call this description2. > > I would like to have both descriptions. Is this possible, and could you > explain how to get this? > > Basically I want to make an additional column. Now I have RefSeq ID, > GeneSymbol and description1. I want to add another column with description2. > > Thank you. > Anton > > On Sat, Jun 30, 2012 at 9:09 AM, Brooke Rhead <[email protected]> wrote: > >> Hi Anton, >> >> RGD replaced UCSC Genes, not RefSeq Genes, so you are right that you do >> not need the RGD tables at all. The RefSeq ID and symbol are contained in >> the refGene table. The description is in a table called "description," >> which can be connected to refGene via the gbCdnaInfo table. To do this in >> the Table Browser, select the rn4 RefSeq Genes track, then: >> >> table: refGene >> region: genome (or whatever you want to limit the output to) >> >> output format: selected fields from primary and related tables >> >> Hit "get output" and scroll down to the Linked Tables section. Select the >> gbCdnaInfo table and hit "allow selection from checked tables." Once you >> have done that, you should be able to scroll down again and select the >> "description" table. >> >> Now select the name and name2 fields from refGene, and the name field from >> description and hit "get output". You should get the output you are >> looking for. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
