Question: Need help with "SnpEff" tool
0
gravatar for barnabe
3.6 years ago by
barnabe0
United States
barnabe0 wrote:

 


 

Tool name: SnpEff
Tool version: 1.0
Tool ID: toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/pcingola/snpe

I would like to have my work genome (Anopheles-darlingi-Coari_BASEFEATURES_AdarC3.2.gff3.gz) as a reference here, how could I have it done?

Thanks in advance.

snpeff • 858 views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.6 years ago by barnabe0
0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This is correct, this database is not supported by the tool on the public Galaxy Main instance (http://usegalaxy.org).

To use it with your genome, a local or cloud Galaxy would be needed: http://wiki.galaxyproject.org/BigPicture/Choices

Then install the tool from the Tool Shed and add in appropriate reference annotation.

Check the SnpEff web site first to ensure availability: http://snpeff.sourceforge.net/

 

One good choice for the tool is this Tool Shed repository (register and/or log into the Tool Shed to see full details):
http://toolshed.g2.bx.psu.edu/view/iuc/snpeff
It includes references to the appropriate Data Managers to install the annotation 

Best, Jen, Galaxy team

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 130 users visited in the last hour