Question: Quickest Way To Get Human Gene Symbols From Refseq Build 37
2
gravatar for Fred Fleche
6.6 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

Hello,

I was wondering what is the quickest way to get a listing of the human Gene Symbols from Refseq Build 37. Thannks in advance for your suggestions.

Fred

gene refseq human • 4.7k views
ADD COMMENTlink modified 2.9 years ago by Rashedul Islam320 • written 6.6 years ago by Fred Fleche4.3k
7
gravatar for Pierre Lindenbaum
6.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:
 curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz" |\
   gunzip -c | cut -d '        ' -f 13 |\
   sort -u
ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Pierre Lindenbaum123k
3

Why not "sort -u" instead of "uniq | sort | uniq"? http://unixhelp.ed.ac.uk/CGI/man-cgi?sort

ADD REPLYlink written 6.6 years ago by zx87548.2k

you're right !

ADD REPLYlink written 6.6 years ago by Pierre Lindenbaum123k

obviously, a single command is much quicker than a few clicks on a web browser.

ADD REPLYlink written 6.6 years ago by Jorge Amigo11k

Thanks a lot Pierre. In the meantime I was looking in the ftp directory at NCBI without finding a nice tab delimited file that would fit my needs. Very sincerely. Fred

ADD REPLYlink written 6.6 years ago by Fred Fleche4.3k
2
gravatar for deanna.church
6.6 years ago by
deanna.church1.1k
Bethesda, MD
deanna.church1.1k wrote:

RefSeq and Gene work with HGNC to get correct gene nomenclature on the NCBI annotation. NCBI is now making GFF files for each annotation run (current run is annotation run 104). You can find the files here: ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/

The name attribute on the 'gene' lines is the HGNC name, if one exists. If not, it will typically be a 'LOC' designator that is used as a placeholder until HGNC can name it.

ADD COMMENTlink written 6.6 years ago by deanna.church1.1k
1
gravatar for Jorge Amigo
6.6 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

when it comes to gene nomenclature I always trust the most the HUGO Gene Nomenclature Committee (HGNC), which provides an always up-to-date gene list here, although you may find more specific information at their downloads section.

but anyway, if I would have to look for a plain list of all current gene symbols I would go to to BioMart, select the latest gene database available (currently Ensembl Genes 69), not create any filter, and select only the "associated gene name" at the attributes section.

ADD COMMENTlink written 6.6 years ago by Jorge Amigo11k
0
gravatar for Rashedul Islam
2.9 years ago by
Canada
Rashedul Islam320 wrote:

You can get this from UCSC table browser. Select genome version and RefSeq genes for the track. This will give you a table with RefSeq id and gene names.

ADD COMMENTlink written 2.9 years ago by Rashedul Islam320
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