Oops, I just saw Brooke sent a similar answer. Hope we have it covered. - Greg
On 3/9/11 10:44 AM, Greg Roe wrote: > Hi Anton, > > Our table browser doesn't do joins (i.e. can't merge the mm9 and rn4 > data into a single output/list), so your best bet is to use our public > MySQL server: > http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 (last section on > page) > > This query (or something similar) should get you what you need... > > SELECT mm9.refGene.name AS "mm9GeneID", > mm9.refGene.name2 AS "mm9GeneName", > rn4.kgXref.geneSymbol AS "rn4GeneName", > rn4.refGene.name AS "rn4GeneID" > FROM mm9.refGene, rn4.refGene, rn4.kgXref > WHERE mm9.refGene.name2 = rn4.kgXref.geneSymbol > AND rn4.kgXref.refSeq = rn4.refGene.name > ORDER BY mm9GeneName; > > Just let me know if you have any additional questions. > > - > Greg Roe > UCSC Genome Bioinformatics Group > > > > On 3/7/11 8:07 PM, Anton Kratz wrote: >> Hi Greg, >> >> thanks; I do not wish to use Galaxy though, as I need such a table of mouse >> RefSeq<-> rat RefSeq as part of an analysis pipeline for comparisons >> between many such lists, which I have written in Perl and which in turn call >> other scripts, R, etc... so including a manual step involving Galaxy is not >> feasible. >> >> What I need is a plain, tab-separated list of mouse RefSeqs and their >> corresping rat RefSeqs, or vice versa. >> >> Could you please explain a little more detailed how to get such a list with >> the table browser? >> >> What I tried, in the table browser, I select: >> clade: Mammal, genome: Mouse, assembly: July 2007 (NCBI37/mm9) >> group: Genes and Gene Prediction Tracks, track: RefSeq Genes >> table: kgXref >> output format: selected fields from primary and related tables >> >> Then click on Get Output. >> >> On the next page (with areas "Select Fields from mm9.kgXref" and "Linked >> Tables"), is where I am stuck. >> >> Anton >> >> On Tue, Mar 8, 2011 at 8:27 AM, Greg Roe<[email protected]> wrote: >> >>> Hi Anton, >>> >>> Yes, you can use the table browser (with the refSeq> kgXref table) to get >>> the gene symbols for both lists and compare. Though, Galaxy makes this a >>> bit more automated (http://main.g2.bx.psu.edu/). >>> >>> Go to Galaxy and click Get Data> UCSC >>> Main<http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=http%3A//main.g2.bx.psu.edu/tool_runner&tool_id=ucsc_table_direct1&hgta_compressType=none&sendToGalaxy=1&hgta_outputType=bed>table >>> browser (upper left). Select the genome, assembly, etc, for rat and >>> use refSeq with the kgXref Table. It will show you UCSC's table browser in >>> the process, and paste your list of gene identifiers in. The "send output to >>> Galaxy" box should be checked by default. When you click output it will >>> allow you to send the output to Galaxy. Then do the same for mouse. Once >>> both data sets are there, you can use Galaxy's "Join, Subtract and Group" >>> tool to compare the data sets ("Compare Two Data sets" tool). Just join them >>> on the geneSymbol column. Your output should then be a list of genes they >>> have in common. >>> >>> Let me know if you have any additional questions. >>> >>> - >>> Greg Roe >>> UCSC Genome Bioinformatics Group >>> >>> >>> >>> On 3/7/11 2:25 AM, Anton Kratz wrote: >>> >>> Dear UCSC team, >>> >>> I have a list of some RefSeq-genes in mouse, and a list of some RefSeq-genes >>> in rat. >>> >>> I want to find out which genes are present in both lists. But I can not just >>> compare the identifiers, as the genes have different IDs in the two species. >>> >>> For example, Grid2 (glutamate receptor, ionotropic, delta 2) in rat would >>> have the identifier NM_024379 and be located at chr4:92642427-94054757, >>> while in mouse it would be NM_008167 at chr6:63206851-64616273. Still >>> NM_024379 in rat is the "same" as NM_008167 in mouse. >>> >>> What is the best approach to find the same genes in two different lists of >>> mouse and rat as described? Is it possible to get a list of equivalent >>> RefSeq identifiers in mouse and rat throught he table browser? >>> >>> Thanks, >>> Anton >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
