Fetching hg19 with Data manager - UCSC's DBKEY for source FASTA?

Question: Fetching hg19 with Data manager - UCSC's DBKEY for source FASTA?

3.3 years ago by

vebaev • 130

vebaev • 130 wrote:

Hi,
I'm trying to get the hg19 genome, if I select only the genome from the dropdown menu it gives me an error, so probably wants UCSC's DBKEY for source FASTA field filled. Is there a table with genomes and their values for this field somewhere?

genome data_manager • 1.3k views

ADD COMMENT • link •

modified 3.3 years ago by christophe.habib • 340 • written 3.3 years ago by vebaev • 130

3.3 years ago by

christophe.habib • 340

France

christophe.habib • 340 wrote:

Hi Ve379,

Did you simply try "hg19" as DBKEY for UCSC?

ADD COMMENT • link written 3.3 years ago by christophe.habib • 340

I just tried hg19, but unfortunately I end up with error - This tool was disabled before the job completed.

ADD REPLY • link written 3.3 years ago by vebaev • 130

3.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Known reference genomes have the dbkey in the description field of the "builds list". This is what is found under the list of reference genomes/builds on the Upload tool form or under Edit Attributes (click on the pencil icon for a dataset). You can explore these at http://usegalaxy.org since we preloaded the same list of builds onto Cloudman and locals.

On the form, are you certain that the field you are filling out is not the genome "source"? Dbkey is one field, source is another. Source is the data provider - each has a specific data structure and this informs the tool about how to retrieve the data. For UCSC, enter "UCSC".

Updated: the prior loading issue was NOTwith hg19 (my mistake). Both hg19 and hg38 should load from UCSC fine.

Best, Jen, Galaxy team

ADD COMMENT • link modified 3.3 years ago • written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »