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Question: visualisation of VCF file,
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gravatar for sara.mehrabi
18 months ago by
sara.mehrabi • 40
Sweden
sara.mehrabi • 40 wrote:

Hi All,

I have a VCF file (1GB), in which 20 samples were compared on local server. I want to visualise the data, but its impossible. i cirdna and IGV. errors on local server: cirdna: Uncaught exception: Assertion failed, raised at ajmem.c:251 IVG: There was a conflict when trying to complete your request. Error generating display_link: A data display parameter is in the error state: bgzip_file and some times it does not work and says, This site can’t be reached

errors on galaxy server cirdna the same error as local server IVG: first work a little bit then ends up with This site can’t be reached

I have one more question, how one can add more Type of model organism in circos on local server?

thanks a lot in advance.

Best, Sara
snp • 607 views
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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 18 months ago by sara.mehrabi • 40

Hi Sara, I have your bug report from yesterday. More feedback soon. Thanks, Jen, Galaxy team

ADD REPLY • link modified 18 months ago • written 18 months ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for Jennifer Hillman Jackson
18 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

VCF format is not an accepted input format for this tool. Please see the underlying tool documentation for the expected format (it is custom and must be created by the user): http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/cirdna.html

Alternative graphing options for VCF data will be listed under the "Visualize" icon's menu within the expanded dataset. Some will require that the database metadata assignment is made. Since you are using a custom genome, this means that you should promote that custom genome to a custom build and then assign the new database dbkey.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k
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