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Have NGS data? Want to use Galaxy? Where to start.

Preparing for an NGS experiment 

Step1.  Inquiry about NGS data generation & data analysis requirements

·       Client contacts the BMGC for sequencing strategy

·       Client contacts MSI-RISS for upcoming analytical support request

o   To: help@msi.umn.edu

Subject line: RISS: Support Request – Researcher’s last name

Cc: lambl001@umn.edu

The NGS experiment starts 

Step2.  BMGC received biological sample for NGS

·       Client provides BMGC with MSI user account name 

Clients will need an MSI user account to access their data.

As part of new standard procedures, all NGS data generated by the BMGC for a UofM client will be pushed into that client’s MSI user account. New storage space has been allocated to support this process. There, NGS data will be ready for analysis from within the Galaxy framework (http://galaxy.msi.umn.edu) as well as using any other tools supported by MSI.

Step3.  If no MSI user account is available, the researcher will request the creation of one.

Two options:

1.     Add a new member to an existing MSI principal investigator’s project or group

MSI principal investigator group owner will go to myMSI  an choose “Manage Accounts in my Groups” to add new group member

2.     Create a new MSI principal investigator’s project or group.

Download the Account Form (Word format compatible) and follow directions


Indicate the members of that will belong to that group. Every individual with access to MSI resource will have his/her own user account and password under that MSI principal investigator’s group.

Step4.    BMGC notifies clients when data is ready for analysis in client’s MSI user account.

BMGC will e-mail its clients when the data are ready and sequencing run report.

All files ownership and access permissions are now controlled by the client and are the client’s responsibilities.  All sharing and access controls can easily be set up from the Galaxy framework.


Using Galaxy 

·       Check the list of Genome Indexes https://sites.google.com/a/umn.edu/galaxy-umn/tasks/genomes to see if the reference genome you'll be using is already loaded into Galaxy. If not, submit a request to have it added.

·       Any question or comments about Galaxy.  Send email:

o   To: help@msi.umn.edu

Subject line: Galaxy – About your question or problem

Cc: lambl001@umn.edu


·       Point of contact. 

o   Anne-Francoise Lamblin   Tel: ext. 5-7414