Hello, Pierre.

You can actually accomplish this using our Table Browser. If you're
unfamiliar with the Table Browser, please see the User's Guide at

1. From http://genome.ucsc.edu, select "Tables" from the blue navigation bar
at the top of the screen.

2. Select the following options:
Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Prediction Tracks
Track: UCSC Genes
Table: knownGene
Region: Select either "genome" for the entire genome or specify a region
next to "position" 
Identifiers: If you already have a list of identifiers you want to convert,
you can click "paste list" or "upload list" to enter them. Otherwise, the
Table Browser will output every UCSC Gene contained in the region you
specified above.
Output format: selected fields from primary and related tables

3. Click the "get output" button

4. In the "Select Fields from hg19.knownGene" section, check the "name"

5. In the "hg19.kgXref fields" section, check the "geneSymbol" checkbox

6. Click the "get output" button

Please contact us again at genome@soe.ucsc.edu if you have any further

Steve Heitner
UCSC Genome Bioinformatics Group

-----Original Message-----
From: genome-boun...@soe.ucsc.edu [mailto:genome-boun...@soe.ucsc.edu] On
Behalf Of Bushel, Pierre (NIH/NIEHS) [E]
Sent: Friday, March 30, 2012 12:07 PM
To: 'genome@soe.ucsc.edu'
Subject: [Genome] How to convert a UCSC gene name/alignID to a gene symbol
gene name

How do I use R and possibly the BSgenome Bioconductor package to convert a
UCSC gene name/alignID such as uc001bvd.3 to a gene symbol and gene
name/description such as MARCKSL1 and Homo sapiens MARCKS-like 1 (MARCKSL1),
Genome maillist  -  Genome@soe.ucsc.edu

Genome maillist  -  Genome@soe.ucsc.edu

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