Searching for RefSeq genes with HUGO IDs in the table browser

[Chris Penkett]

Hi UCSC browser folks,

I'm searching for a gff of RefSeq genes and using the paste list option in the table browser:

http://genome-euro.ucsc.edu/cgi-bin/hgTables

These are the main options set:

assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions
track: RefSeq Genes
table: refGene

When I search for a list with HUGO names like this:

ACD
ANKRD26
BRCA1
BRCA2

It complains:

"Note: 4 of the 4 given identifiers have no match in table refGene, field name. Try the "describe table schema" button for more information about the table and field. ..."

When I last used this feature in May, it seemed to work.  Has anything changed or did I use a different track before?  The thing is the RefSeq genes return a different gff file than the UCSC genes (chrom has moved from column 3 to column 2), which no longer works with my scripts:

RefSeq headers:

#bin    name    chrom    strand    txStart    txEnd    cdsStart    cdsEnd    exonCount    exonStarts    exonEnds    score    name2    cdsStartStat    cdsEndStat    exonFrames
224    NM_001301685    chr2    -    159195104    159313265    159195233    159312951    7    159195104,159195501,159196753,159197109,159201726,159214960,159312926,    159195419,159195597,159196905,159197192,159201830,159215082,159313265,    0    CCDC148    cmpl    cmpl    0,0,1,2,0,1,0,

UCSC headers:

#name    chrom    strand    txStart    txEnd    cdsStart    cdsEnd    exonCount    exonStarts    exonEnds    proteinID    alignID
uc001uua.1    chr13    +    32889616    32907524    32899265    32907523    10    32889616,32890558,32893213,32899212,32900237,32900378,32900635,32903579,32905055,32906408,    32889804,32890660,32893462,32899321,32900287,32900419,32900750,32903629,32905167,32907524,    E9PIQ1    uc001uua.1
uc001uub.1    chr13    +    32889616    32973809    32890597    32972907    27    32889616,32890558,32893213,32899212,32900237,32900378,32900635,32903579,32905055,32906408,32910401,32918694,32920963,32928997,32930564,32931878,32936659,32937315,32944538,32945092,32950806,32953453,32953886,32954143,32968825,32971034,32972298,    32889804,32890664,32893462,32899321,32900287,32900419,32900750,32903629,32905167,32907524,32915333,32918790,32921033,32929425,32930746,32932066,32936830,32937670,32944694,32945237,32950928,32953652,32954050,32954282,32969070,32971181,32973809,    NP_000050    uc001uub.1
uc031qky.1    chr13    +    32928997    32936830    32929166    32936796    2    32928997,32936659,    32929425,32936830,        uc031qky.1
uc031qkz.1    chr13    +    32945092    32953652    32945092    32945092    2    32945092,32953453,    32945237,32953652,        uc031qkz.1

Best wishes,
Chris

--

Chris Penkett
Head of Pipelines for NIHRBR-RD

NIHR BioResource Rare Diseases (NIHRBR-RD)
F31, Department of Haematology
University of Cambridge & NHS Blood and Transplant
NHSBT Building
Long Road
Cambridge CB2 0PT

Tel: 01223 588092
Email: cj...@cam.ac.uk
WWW: https://bioresource.nihr.ac.uk/rare-diseases/rare-diseases/

[Cath Tyner]

Hi Chris,

Thanks for using the UCSC Genome Browser and for describing the issue you experienced with the refGene table in the Table Browser. We believe that there was a momentary issue causing this which is now resolved. Can you please try your query again? Please respond to this forum if you continue to experience this problem so that we can assist you!

Thank you again for your inquiry and for using the UCSC Genome Browser. 

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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[Chris Penkett]

Hi Cath,

Yes it seems to work now!

Thanks,
Chris