Errors with CCDS queries when using hg19 assembly

[Adzhubey, Ivan A.]

Hi,

Looks like the mapping of transcripts between hg19 knownGene and CCDS
tracks is broken. When clicking on the CCDS identifier in the Genome
Browser window, an error message is produced, eg:

Warning/Error(s):

    query not found: NOSQLINJ select spID from kgXref where
kgID='uc003vmb.2'

Similar error persists for all CCDS entries I have tried. These same
CCDS identifiers are correctly processed when using hg38 assembly version.

Best,

Ivan

--
Ivan Adzhubey, Ph.D.
Research Associate
Department of Biomedical Informatics
Harvard Medical School
10 Shattuck Street, Suite 514
Boston, MA 02115
tel: (617) 432-2144
fax: (617) 432-0693
web: https://sunyaevlab.hms.harvard.edu/wiki/!web/start

[Matthew Speir]

Hello, Ivan.

Thank you for bringing this issue to our attention.

We've dropped the ccdsKgMap table, which contained some outdated mappings, so clicking on items in the CCDS track should be functioning now. The links from CCDS to other sources, e.g. RefSeq, Vega, or Ensembl, are still functioning. The knownGene table for hg19 uses GNECODE/Ensembl IDs now, so using the Ensembl link should be equivalent.

If you have any further questions, please reply to gen...@soe.ucsc.edu. 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.

---

Matthew Speir

UCSC Genome Browser, User Support

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[Adzhubey, Ivan A.]

Hi Matthew,

Thank you for your reply and for confirming my understanding of the problem. However, is there any way to map hg19 GENCODE gene identifiers to the corresponding CCDS IDs? This was possible to do in SQL using ccdsKgMap table but it includes now outdated/obsolete knownGene identifiers in its hg19 version, thus this mapping no longer works. The corresponding hg38 table however, has been updated with the actual GENCODE identifiers. Would it be possible to also update the hg19 version at some point?

Thanks,

Ivan

[Matthew Speir]

Hello, Ivan.

If you turn on the "GENCODE Versions" track under "Genes and Gene Predictions" and click on a gene/transcript, e.g. ENST00000297261.7_7, you should see the CCDS identifier: https://genome.ucsc.edu/cgi-bin/hgc?db=hg19&c=chr7&l=155592222&r=155605565&o=155592673&t=155605157&g=wgEncodeGencodeBasicV47lift37&i=ENST00000297261.7_7.

This info comes from the table wgEncodeGencodeAttrsV47lift37, which has a column ccdsId.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. 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.

---

Matthew Speir

UCSC Genome Browser, User Support