List of 'not found' identifiers
Thomas Cullup
Hi
I’m hoping you can help; I am trying to submit a list of gene identifiers to the table browser in order that I can pull out exon start and end coordinates. It seems that some of the identifiers are not found:
- “Note: 8 of the 142 given identifiers (e.g. UQCC2) 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.
However, without knowing which 8 in the above query (other than UQCC2) have no match, it is hard for me to correct this. It would be great if all the unmatched identifiers are given, so that I know which I need to check/change.
Is this possible please?
Thanks very much for your help
Tom
Thomas Cullup
Clinical Scientist
Regional Molecular Genetics Laboratory
Great Ormond Street Hospital for Children NHS Foundation Trust
Level 6 York House
37 Queen Square
London
WC1N 3BH
Tel: 020 7762 6877
Fax: 020 7813 8196
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Steve Heitner
Hello, Tom.
This is actually not the first time we’ve received a report like this. A feature request was opened to add this feature, but it has yet to be implemented. I will re-open an internal discussion to see if we can move this up in priority.
In the meantime, there is a workaround. This question has also been asked at Biostars (https://www.biostars.org/p/93112/). One of the recommended solutions was to create a diff of your own list of IDs and the list of IDs output by the Table Browser. One possible method is described in detail at http://linux.die.net/man/1/comm.
Please contact us again at gen...@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Steve Heitner
UCSC Genome Bioinformatics Group
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