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Question: hg19 genome from USCS not visible in Visualization?
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gravatar for vebaev
3.3 years ago by
vebaev • 130
vebaev • 130 wrote:

I have the hg19 fetched automatically from USCS, I have the genome as well as made the indexed for bowtie. I have mapped some reads to it with bowtie and worked fine. 

But when I go to Visualization I do not see it under Reference genome build (dbkey): 
(nevertheless I see the Tomato genome which I got fetched from custom sequence)

Data Manager: all_fasta 
value    dbkey    name    path
hg19    hg19    Human Feb. 2009 (GRCh37/hg19) (hg19)    /galaxy-central/tool-data/hg19/seq/hg19.fa

tomato24    tomato24    Solanum lycopersicon (tomato ITAG2.40)    /galaxy-central/tool-data/tomato24/seq/tomato24.fa

 
visualization hg19 • 945 views
ADD COMMENT • link •
modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by vebaev • 130
0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Has hg19 included in your "builds.txt" list? Perhaps it was not selected/created when the genome was installed on your instance using the fetch genome Data Manager? 

The builds list addition can be confirmed by looking in either of these two locations:

  1. Edit Attributes form: On the first tab, search the "Database/Build:" list by the keyword "hg19. This form is found by clicking on the upper right corner pencil icon inside of any dataset.
  2. Upload tool: Search the same list. This tool is at the very top of the left tool panel.

Hopefully this helps to troubleshoot. Jen, Galaxy team
ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

I think the Attributes are ok, so there must be something else:

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

I think I found something:
the hg19 is missing in dbkeys data manager, as I fetched the reference genome with "Reference Genome" data manager and not with "Create DBKey and Reference Genome".
Do you know how to fix it?

Data Manager: all_fasta 
value    dbkey    name    path
hg19    hg19    Human Feb. 2009 (GRCh37/hg19) (hg19)    /galaxy-central/tool-data/hg19/seq/hg19.fa

Tomato24    Tomato24    Solanum lycopersicon 2.40    /galaxy-central/tool-data/Tomato24/seq/Tomato24.fa

tomato24    tomato24    Solanum lycopersicon (tomato ITAG2.40)    /galaxy-central/tool-data/tomato24/seq/tomato24.fa​


Data Manager: __dbkeys__ 
value    name    len_path
Tomato24    Tomato 2.40    /galaxy-central/tool-data/Tomato24/len/Tomato24.len
tomato24    tomato24    /galaxy-central/tool-data/tomato24/len/tomato24.len
ADD REPLY • link modified 3.3 years ago • written 3.3 years ago by vebaev • 130
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