Question: hg19 genome from USCS not visible in Visualization?
0
gravatar for vebaev
2.4 years ago by
vebaev130
Bulgaria
vebaev130 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 • 697 views
ADD COMMENTlink modified 2.4 years ago by Jennifer Hillman Jackson23k • written 2.4 years ago by vebaev130
0
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson23k

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

ADD REPLYlink written 2.4 years ago by vebaev130

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 REPLYlink modified 2.4 years ago • written 2.4 years ago by vebaev130
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