Dear UCSC Genome Bioinformatics Group, I would like to extract 3'-UTRs from Rat genes. I've tried exporting from the UCSC table - following these directions: https://lists.soe.ucsc.edu/pipermail/genome/2008-May/016356.html
I uploaded a list of 22062 genes (NM_ format) and went to export 3'-UTR. Unfortunately I get an error: "Note: 16094 of the 22062 given identifiers (e.g. NM_146082) 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." I have a gene list both as gene names, gene symbols and also accession numbers and all give a similar report... i.e it doesn't seem to recognise the identifiers I upload. I've checked the numbers/symbols that I'm uploading - and they are real and do exist. It seems there is a list of only 7816 genes in the known gene database for Rat - Could this be true? I got this number by simply not uploading any genes and went straight to 'get output' from 'Known genes' and got the 3'-UTRs from all rat genes. This list is also ~2000 genes longer than when I uploaded my list of genes (see above). Many thanks in advance for any help you can give, Sam _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
