http://hgdownload.cse.ucsc.edu/downloads.html#human
tohttp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
But there are many files in the link above, and I am not sure which file represents the complete set of annotations.Pankaj Agarwal, M.S
Bioinformatician
Bioinformatics Shared Resource
Duke Cancer Institute
Duke University
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Hi,
Thank you for your clear instructions. I had a quick follow up question.
Can you please provide some information on what are the basic differences in the annotation provided by Ensembl and UCSC, in general how they are produced and, in particular, what is the basic differences in their content and data structure.
Thank you,
- Pankaj
From: Matthew Speir [mailto:msp...@soe.ucsc.edu]
Sent: Friday, April 11, 2014 3:49 PM
To: Pankaj Agarwal
Subject: Re: [genome] Human Reference Genome Annotation GTF download
Hi Pankaj,
Thank you for your question about getting a gene annotation file from the UCSC Genome Browser. Unfortunately, we do not provide a download for the UCSC Genes annotation track in GTF format. You can however generate this file yourself using the Table Browser,
http://genome.ucsc.edu/cgi-bin/hgTables. To get this information from the Table Browser, use the following steps:
1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables
2. Select the following options:
clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions
track: UCSC Genes
table: knownGene
region: Select "genome" for the entire genome.
output format: GTF - gene transfer format
output file: enter a file name to save your results to a file, or leave blank to display results in the browser
3. Click 'get output'.
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 Bioinformatics Group
On 4/10/14, 11:06 AM, Pankaj Agarwal wrote:
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