Hi Greg, Thanks for the detailed information. Finally I have 8726 "NM" id which does not match in UCSC... ******example** NM_001002792 NM_001003669 NM_001003914 NM_001003930 NM_001004138 NM_001013392 NM_001013793 NM_001013800 NM_001013808 NM_001014425 NM_001024731 NM_001024838 NM_001024839 NM_001024840 NM_001024849 NM_001025208 NM_001025241 NM_001030310 NM_001033001 NM_001033127 NM_001033151 NM_001033160 NM_001033198 ******* Thanks, Shibu
________________________________________ From: Greg Roe [[email protected]] Sent: 08 February 2011 19:56 To: John, Shibu Cc: [email protected] Subject: Re: [Genome] About NCBI gene coordinate from Gene ID or refseqID 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
