Hello, Anton. The purpose of the rgdGene2Xref table is to combine the contents of several of the supporting tables, but you are correct that there appears to be some disagreement between the various fields of rgdGene2Xref. Thank you for bringing this to our attention. We will certainly look into this issue.
The best solution here would be to link to the individual tables that contain the information you are interested in. Based on your description of your desired output, follow Luvina's previous instructions, but in the step where she instructed you to link to regGene2Xref, you will link to rgdGene2ToDescription, rgdGene2ToRefSeq and rgdGene2ToSymbol. For your output, you will want to select rn4.rgdGene2.name, rn4.rgdGene2ToDescription.value, rn4.rgdGene2ToRefSeq.value and rn4.rgdGene2ToSymbol.geneSymbol. You also mentioned that you would like coordinates included in your output. There are several coordinate fields in the rn4.rgdGene2 table. Select the fields appropriate to your needs. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Anton Kratz Sent: Monday, May 28, 2012 10:00 PM To: UCSC Genome Browser Mailing List Subject: [Genome] [info and infoType don't match] Re: kgXref, rn4 Dear UCSC team, thank you for your answer; I have a follow-up question. I followed your instructions to generate a table with these three fields: #rn4.rgdGene2.name rn4.rgdGene2Xref.infoType rn4.rgdGene2Xref.info How is one supposed to make the correct relation between the comma-separated elements in rn4.rgdGene2Xref.infoType and rn4.rgdGene2Xref.info? I believe the idea is that the entries for the infoType and info fields are themselves comma-separated fields, and are in the same order from left to right?! But this is not actually the case (examples see below). I want to parse this data with my own Perl scripts. I do not understand how one can (in a Perl or Python script) figure out from this data which of the entries in rn4.rgdGene2Xref.infoType belongs to which of the entries in rn4.rgdGene2Xref.info. For example, the first line: RGD:1565877 GeneID,ID,Name,gene, 499014,RGD1565877,Zdhhc14, The field "infoType" has four entries, "info" has three entries. Or this entry: RGD:1303141 GeneID,ID,Name,Note,gene, 308291,Phactr2,RGD1303141,Phactr2,member of a family of proteins that bind protein phosphatase 1 and cytoplasmic actin%3B may play a role in regulation of the actin cytoskeleton,Phactr2, In this case the comma-separated fields seem to be mixed up: GeneID 308291 ID Phactr2 Name RGD1303141 Note Phactr2 gene member of a family of proteins that bind protein [...] ??? Phactr2 info and infoType do not match, and I get the actual Gene Symbol three times... Could you please explain how to parse a table, which has been generated as described in the previous emails (please see below)? What I want to generate is a table with RGD-Gene ID and coordinates, Protein encoded, Description in TAB-separated fields so that I can parse this from a script. best regards, Anton On Fri, Apr 27, 2012 at 3:00 AM, Luvina Guruvadoo <[email protected]>wrote: > Hi Anton, > > The rgdGene2Xref table should provide the information you are looking for. > In the Table Browser, make the following selections: > > track: RGD Genes > table: rgdGene2 > output format: selected fields from primary and related tables > > Click 'get output'. Scroll down and select rgdGene2Xref from the > Linked Tables section and click 'Allow Selection From Checked Tables". > From here, you can select fields such as infoType and info from rn4.rgdGene2Xref. > > I hope this helps. Please contact us again at [email protected] if > you have any further questions. > > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > > > On 4/26/2012 1:17 AM, Anton Kratz wrote: > >> Dear UCSC team, >> >> I am trying to make a table that contains RefSeq IDs and various >> other information. >> >> I can not find the table kgXref anymore, when I select RefSeq in the >> table browser. >> >> I assume that RefSeq has been superseded by RGD, but there is a lot >> of guessing involved regarding the way the tables are linked. >> >> Could you please let me know about the relevant changes? >> >> I'd like to make a table with RefSeq pointing to gene symbol, >> description and maybe other type of info. >> >> thanks, >> Anton >> ______________________________**_________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.so >> e.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
