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Question: Error using DataManager to fetch a reference genome
0
gravatar for jchen015
3.8 years ago by
jchen015 • 80
Singapore
jchen015 • 80 wrote:

Hi guys

So I was trying to leverage on Data Manager functionality to perform the addition of reference genome for future data visualization.

I followed the steps taught by Daniel through the video link "https://vimeo.com/74265510".

However, when I try to fetch a reference genome (reference_genome_hg19_1.png) for hg19, I encounter an error which doesnt specify the root of the cause (reference_genome_hg19_3.png).

May I know what is the reason? To perform data manager, do i have to perform some activities prior to it?

Photo links: https://www.dropbox.com/sh/dsjj042we8motu2/AAAKjk0JaVppU3nERf3SxCb-a?dl=0

 

Regards.

Julius
datamanager hg19 • 1.3k views
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modified 3.7 years ago • written 3.8 years ago by jchen015 • 80
1
gravatar for Jennifer Hillman Jackson
3.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Try using this Data Manager to create a new dbkey and all the associated data for visualization (the .len file, etc.):
https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_fetch_genome_dbkeys_all_fasta
ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k

Followup related to: How to leverage on an existing fasta file as a reference genome build (dbkey)

ADD REPLY • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for jchen015
3.8 years ago by
jchen015 • 80
Singapore
jchen015 • 80 wrote:

Hi guys. Managed to fetched the reference genome after Daniel asked me to try data manager on the main tool shed rather than the test tool shed.

 

Another question over here, after i indexed the sam fasta file, when i go into Visualization tab, under the reference genome build (dbkey), shouldnt I have an available genome build after performing the data manager steps?

Photo links: https://www.dropbox.com/sh/9yl546419dc4m5h/AACCJ1K7ITtO18keFLrgDvVra?dl=0

 

 

Or is there any other activities which I should perform still ?
ADD COMMENT • link written 3.8 years ago by jchen015 • 80
0
gravatar for jchen015
3.7 years ago by
jchen015 • 80
Singapore
jchen015 • 80 wrote:

Hi all.

any idea what is the issue over here?

 

Regards,

Julius
ADD COMMENT • link written 3.7 years ago by jchen015 • 80
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