Hi Francisco, Not all of the identifiers in your list are in our hg18 database.
It appears that you may be trying to use identifiers that are in our hg19 database on the hg18 assembly. When you are in the table browser with the "knownGene" table selected click on the "describe table schema" button and then for the name row click on the "values" link to see all of the valid ids allowed for that table. The links below show all the "Name" values for the knownGene table. You will see that "uc010flp.2" is in the values list for hg19 and not hg18. This is likely the case for the other identifiers you are trying to use. Name values for hg18: http://genome.ucsc.edu/cgi-bin/hgTables?hgta_database=hg18&hgta_histoTable=knownGene&hgta_doValueHistogram=name Name values for hg19: http://genome.ucsc.edu/cgi-bin/hgTables?hgta_database=hg19&hgta_histoTable=knownGene&hgta_doValueHistogram=name I hope this helps clarify things for you. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Francisco Pisciottano <[email protected]> Date: Mon, Jan 23, 2012 at 8:02 AM Subject: [Genome] GO term genes to hg18 positions in the browser To: Hello, my name is Francisco, I'm trying to find the positions corresponding to list of genes associated to a determined GO term. I can previously get any kind of IDs for the list of genes that correspond to a GO term from data mining (anyway, if this can also be done with Table Browser I would like to try it to see if it's better than what I'm using now), but what I really need is to get the position in the 2006 assembly ('hg18') for all these genes. I've been reading the Table Browser User's Guide and exploring the questions mail archives, so I've tried to solve my question with what I found there, but there's something I must be doing wrong, because I keep getting messages like: *Error(s):* - Note: 69 of the 80 given identifiers (e.g. uc010flp.2) have no match in table knownGene, field name or in alias table kgAlias, field alias. Try the "describe table schema" button for more information about the table and field. Although most times the total number of genes pasted in the list report this problem. I'd very much appreciate your help and some advise. Thank you, Francisco _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
