Header line for hg19 refGene

[Shi, Jiajun]

Dear Sir/Madam,

 

I could not find a header line to annotate the columns in the refGene.txt file.  I need a file with gene name, chromosome region in hg19.

 

Thanks,

Jiajun

 

 

[Brian Lee]

Dear JiaJun,

Thank you for using the UCSC Genome Browser and your question about
finding a header line to annotate the columns in the refGene.txt file.

From the browser home page, www.genome.ucsc.edu, if you click the link
to "Downloads" on the left column you will come to our download
server, http://hgdownload.soe.ucsc.edu/downloads.html. Click "Human"
under the Vertebrates section, and then click the link to the
"Annotation database",
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/. Here you
will find the refGene.txt.gz file for the hg19 assembly.

Just above refGene.txt.gz is the file refGene.sql. If you download
and open this file you will find the column header information you are
seeking.

You can also use our Table Browser to select information from the
refGene table by clicking "Tables" from http://genome.ucsc.edu/, and
using the following settings:

Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Prediction Tracks
Track: refSeq Genes
Table: refGene
Region: genome
Output: all fields from selected table

You could further change the output selection to only "selected
fields" and limit the data to position and gene name. For more
information on the Table Browser, please watch this tutorial:
http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28. Or read the
related help pages:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.

Thank you again for your inquiry and using the UCSC Genome Browser,
if you have further questions please feel free to contact the mailing list
again at gen...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

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[Shi, Jiajun]

Dear Brian,

Thanks a lot for your great help! It helps so very much as I could use the original and most accurate data for my work.

Have a nice day!

Jiajun