[Genome] Genome browser: CpG islands - trouble entering information

david.mossman at studentmail.newcastle.edu.au david.mossman at studentmail.newcastle.edu.au
Thu Oct 18 02:25:47 PDT 2007


Hi,

I'm having troubles using the genome viewer. To be specific I have a list of genes/accession numbers and want to find if there is a CpG island associated with the gene. I couldn't find any answers on the website so I have decided to email for an answer. The details I have entered into the genome viewer are as follows:

clade:Vertebrate, genome:Human, assembley:Mar 06
group:Genes and Gene Prediction Tracks, track:RefSeq Genes
table:refGene
Region:genome
Identifiers: (uploaded my list of accession numbers in here, in .txt format)
Intersection with cpgIslandExt
Output file type: BED

When I upload my file I get a message saying, "Note: some of the identifiers (e.g. NM_138705.2) have no match in table refGene, field name or in alias table refLink, field name. Try the "describe table schema" button for more information about the table and field."

When I submit the info anyway, the next page comes up, I hit 'GET BED' and the next screen tells me, ''No results returned from query".

Could someone please tell me what I am doing incorrectly?
Many thanks,
David


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