Hi Katrina, Thanks for your help. I was doing through refFlat and kgAlias tables. But probably it will be better through knownGenes table. Thanks again.
Lipika On Fri, Aug 27, 2010 at 12:35 PM, Katrina Learned <[email protected]>wrote: > Hi Lipika, > > In my previous email, I forgot to mention which table contains this > information. The UCSC Genes track has two tables that, together, contain the > information you are looking for. The main table, knowGene, contains the > chromosome and position, and the kgAlias table contains the RefSeq protein > accession (NP-XXXXXX). The two tables are linked by the common field, the > known gene ID (knownGene.name & kgAlias.kgID). You can download these tables > from our download server here: > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ > > > Katrina Learned > UCSC Genome Bioinformatics Group > > Katrina Learned wrote, On 08/27/10 09:11: > > Hi Lipika, >> >> The data is available in our downloadable tables, however, we don't have >> an automated way of providing the the RefSeq ID for a set of coordinates. >> You would have to develop code to do retrieve the IDs based on the >> chromosome number and genomic position. >> >> Please don't hesitate to contact the mail list again if you have any >> further questions. >> >> Katrina Learned >> UCSC Genome Bioinformatics Group >> >> >> Lipika Ray wrote, On 08/24/10 13:07: >> >> >>> Dear UCSC genome broser group, >>> >>> I have set of genomic position based on hg18, I like to get the >>> corresponding refseq accession, like 'NP_XXXXXX' - how can I get that >>> using >>> your downloadable tables? >>> One example is like this: >>> >>> Chrom, position, Refseq protein ID >>> 1,878522,NP_056473 >>> >>> So using chromosome number and genomic position, I like to get NP numbers >>> based on hg18. >>> >>> Thanks a lot for any help! >>> >>> Lipika Ray >>> _______________________________________________ >>> 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
