Hi Shibu, >> check the boxes next to "name", "txStart", and "txStop"
Of course I meant "txEnd". ;-) - Greg On 2/8/11 11:56 AM, Greg Roe wrote: > Hi Shibu, > > The easiest way to do this would be to use the Table Browser > (http://genome.ucsc.edu/cgi-bin/hgTables). Select the assembly of > interest, mm9 I assume. The select: > > Group: Genes and Gene Prediction Tracks > Track: RefSeq Genes > Table: refGenes > Region: genome > > Then under identifiers click upload list. You'll need to make a list of > all the gene ids, without all the extra data (ex: NM_020501). You'll > need to remove the version numbering as well. So NM_020501.1 should be > shown as NM_020501, without the .1. The east low-tech way to do this > would be to load your data in a spreadsheet using the pipe as a column > delimiter, removing the extra columns, then doing a find and replace to > remove all the version designations, ".1", etc. Then save the gene ids > to a text file and upload that. > > Then set the output format to "selected fields from primary and related > tables, choose desired file type returned, and click "get output". > > On the subsequent screen, check the boxes next to "name", "txStart", and > "txStop". Click "get output" and you should have the data you need. > > Now, there are about 28,150 rows in that data set. You may have more > refSeq ids because UCSC only displays Accession types that start with > NM_ and NR_. There are several other types, see: > http://www.ncbi.nlm.nih.gov/projects/RefSeq/key.html#accessions. So we > only display a subset of the total. > > Hope that helps! > > Just email the genome list if you have any additional questions. > > - > Greg Roe > UCSC Genome Browser Group > > > > > On 2/6/11 1:31 PM, John, Shibu wrote: >> Hi, >> >> I have a list of (36692) NCBI refSeq id in the following format. (Mouse, >> downloaded on May 2009 ) >> ***** >> gi|10048421|ref|NM_020488.1| >> gi|10048425|ref|NM_020501.1| >> **** >> Is there any way to get the chromosome start, end position of these geneID? >> ( chr6 131636578 131637481 gi|10048425|ref|NM_020501.1|) >> >> I tried to intersect with the "NM_" id with UCSC >> "http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/refGene.txt.gz"; >> ******** >> gi|10048425|ref|NM_020501.1| Tas2r105 NM_020501 chr6 - >> 131636578 131637481 >> ******** >> >> But this "refGene.txt" contains only 28108 id's.. >> >> And I tried to find the gene with Entrez batch finder .. >> ******* >> Id=XM_915912: This record was removed as a result of standard genome >> annotation processing. See the genome build documentation at >> http://www.ncbi.nlm.nih.gov/genome/guide/build.html for further information, >> or contact [email protected]. >> Id=XM_912174: This record was replaced or removed. >> ........ >> ....... >> Received lines: 36692 >> Rejected lines: 17 >> Removed duplicates: 0 >> Passed to Entrez: 36675 >> ********* >> >> It will be a great help that if you can help me to get the chromosome start >> position of these genes or corresponding ENSEMBL gene ID. >> >> Thanks, >> Shibu >> >> _______________________________________________ >> 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
