GenomeSpace Orientation Webinar - Feb. 29, 2016 - Question & Answer session

We received several questions during our Question & Answer session. We've provided the transcribed questions and answers here for ease of use.

GENERAL GENOMESPACE QUESTIONS:
What other tools will GenomeSpace add in the near future?

Is there any requirement of an institutional mail ID to register for Genome Space?
There is no institutional ID requirement to join and use GenomeSpace. GenomeSpace is free to use for all users, regardless of affiliation.

Up to what extent can we upload data (e.g. how many GBs)?
GenomeSpace provides users with 30GB of free cloud storage on an Amazon S3 bucket. You can increase this amount by connecting your private Dropbox, Google Drive, or Amazon accounts.

Is GenomeSpace cluster based? What's the mechanism for users' to wait for their jobs to be processed?
Since GenomeSpace is not a tool itself, it is not cluster-based, and it cannot queue or run jobs.

Can GenomeSpace tools be used from outside the US?
Yes, GenomeSpace tools can be used from outside the US.

What version of Java will I need?
We recommend using the latest version of Java for these tools. To check your Java version, you can use the Java Tester website.

Will I need to install a specific version of R?
No, you do not need to install R or any other software packages to use GenomeSpace.

Does GS provide additional services for NGS analysis beyond Galaxy?


RECIPE & ANALYSIS QUESTIONS:

Why are "recipes" called that?
We gave "recipes" their name because they are fundamental bioinformatic analyses with defined inputs and (ingredients) and outputs, and they follow a specific protocol to complete a short analysis. Like cooking recipes, they can be modified and combined, and serve as a basic guideline to help a user through the analysis process.

How many options do we have to change the analysis settings?
Recipes are simple guidelines to help users through an analysis process. They are written with a specific input, analysis, and output in mind. However, users are welcome to use their own data and follow-along with a recipe, changing parameters where they wish. For example, if a recipe is looking for the top 50 genes in a dataset, and the user is looking for the top 100 genes, the user should feel free to modify parameters in order to achieve their desired result.

How do you ensure that recipes work after future updates to external tools, such as Galaxy, etc.?
We strive to keep recipes up-to-date as much as possible. This includes periodically re-taking screenshots and modifying recipe text to ensure that the step-by-step descriptions are as accurate as possible. We don’t catch all tool updates – so if you find something that appears out of date or isn’t working, please let us know by contacting us.

What is the .gct format?

Is there a module/recipe for cross-species analysis? I.E. convert gct files between human and mouse?
There is no specific recipe for cross-species conversion at the moment. However, a GenomeSpace tool - UCSC Table Browser - has many reference genomes available for a large number of model organisms, which can be used to convert datasets between species.

Can you do miRNAseq analysis? Target genes of miRNAs? Is it possible to do QTL analysis?

WEBINAR QUESTIONS:

Will the webinar be available on-demand for download/record at later time?

Will the next webinar cover different aspects of GenomeSpace?
We strive to cover a variety of topics in our webinars. If you have any suggestions for a topic, please email us.

When is your next webinar?