Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Need help with "SnpEff" tool
0
gravatar for barnabe
4.1 years ago by
barnabe • 0
United States
barnabe • 0 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 • 1.0k views
ADD COMMENT • link •
modified 4.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.1 years ago by barnabe • 0
0
gravatar for Jennifer Hillman Jackson
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour