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
