Question: how to analyze gene expression and Chip-seq data in Galaxy
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gravatar for mayurdoke
6 months ago by
mayurdoke0
mayurdoke0 wrote:

Hello Jennifer,

As per your suggestion, I am going to install Galaxy local and RNACHIPintegrator tool on my computer. Will be the display or interface of a local galaxy as same as Public galaxy server? I have another question regarding gene expression. How can I determine the up and down regulation of genes from Chip-seq data?

Thank you for your support.

chip-seq • 183 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson23k • written 6 months ago by mayurdoke0
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The user interface at the basic level will be the same. The tools and local data is unique to each Galaxy server. Certain functions can also be activated or not (FTP is one example).

Admin training is here: https://github.com/galaxyproject/dagobah-training

You will need to set up your local with the tools and data resources you want to use. There are resources for replicating Main, but this is usually wanted and implemented by an administrator creating a server as a service (local to some group or to be hosted publically). It takes considerable computing resources to fully replicate and support the work that can be done at http://usegalaxy.org and other Public Galaxy sites, even for a single server/user. Many choose to use Cloudman with AWS to build a server with the tools they need and compute resources on demand so that they don't need to invest in hosting it locally.

The analysis questions are big ones without a simple answer. There are many resources, publications, tool & tool manuals, help and message boards, etc focusing on these topics. Reviewing to get the bigger picture is important for any serious analysis.

That said, tutorials for Galaxy are available here: https://galaxyproject.org/learn/ You might find others on the web and/or relevant discussions here at Galaxy Biostars, although most are about the details - troubleshooting and the like.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson23k
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