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
