Hello, The refFlat file would be an appropriate place to search. Make sure that it is downloaded from the hg18 (not hg19) ftp location.
Only SNPs from the reference genomic sequence should be mapped. The RefSeq annotation is based on this assembly. Coordinates from other assemblies, such as the alternate Celera assembly, will not align correctly. If there is not match, then the SNPs have no overlap. You may consider other Gene tracks. Open the browser and examine the tracks in the Gene and Gene Predictions group. UCSC Genes would be the best place to start - it contains RefSeq plus other input sources. The track description provides details about the methods. Some coordinate help: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms And file format help: http://genome.ucsc.edu/FAQ/FAQformat.html Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- [email protected] wrote: > From: [email protected] > To: [email protected] > Cc: [email protected] > Sent: Friday, February 5, 2010 1:43:20 AM GMT -08:00 US/Canada Pacific > Subject: Query about hg18 genomic coordinates > > Dear Jennifer, > > We have a list of SNPs with genomic co-ordinates (both from ncbi, > celera & > ref assemblies) that we would like to get corresponding gene > annotations > for. We don't have the flanking sequence, gene name, ID, gene length, > CDS > or any other information. Currently, we are using build hg18 (ncbi > 36.1). > What file should we search against to look for gene annotations? We > understand the genomic co-ordinates do change with different build > numbers > and hence we would like to search in build 18 only. When we searched > against the genomic regions between column 5&6 in the the refflat.txt > file, for certain SNPs (especially those from celera & ref > assemblies) > don't match to anything in the refflat.txt file. Any suggestions would > be > useful. > > Thank you. > > Rakhi _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
