Question: Reference genome: no options available - use Custom reference genome
0
gravatar for a.donato
17 months ago by
a.donato0
a.donato0 wrote:

Hi,

I am using galaxy and in particular a modified version of a workflow that I found on usegalaxy.org.

Even if in the workflow I have everywhere indicated which one is the reference genome I wish to use, some steps such as the "Realigner target creator" on data coming from the step "Add or replace groups" give me a error because in the using reference genome section there are no options available and I don't know why that's happening and how to fix it.

Can anyone with more experience than me explain me how I should proceed?

Thank you.

Best regards. Alessandra

ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson25k • written 17 months ago by a.donato0
0
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

GATK tools are deprecated in Galaxy. Alternative tools for variant analysis are in our tutorials here: https://galaxyproject.org/learn/

If you do run into a tool that does not have your genome natively indexed on the server you are working on, a Custom reference genome can be used. This is how: https://galaxyproject.org/learn/custom-genomes/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 17 months 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: 172 users visited in the last hour