Question: Using web based platform for analysis
1
gravatar for ChickenRNA
17 months ago by
ChickenRNA50
ChickenRNA50 wrote:

Hi, I am new to the world of NGS bioinformatics. I am not very good with command based programs. I have an RNASeq dataset for 49 samples (paired-end reads). I am wondering if I can do the analyses using the web-based platform if I upload all the data through FTP. I have almost 130 Gb of data. Any help and guidance will be greatly appreciated.

rna-seq • 379 views
ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson23k • written 17 months ago by ChickenRNA50
2
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Galaxy's web based tools can be used for RNA-seq analysis. This tutorial provides an overview: https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq

Your data size may require the use of a local or cloud Galaxy. Please see: https://wiki.galaxyproject.org/BigPicture/Choices

For Support/Help resources, the Galaxy Wiki is a good place to find information: https://wiki.galaxyproject.org/Support

Best, Jen, Galaxy team

ADD COMMENTlink written 17 months ago by Jennifer Hillman Jackson23k

Thank you for providing the resources Jennifer. One more questions, is the local or cloud Galaxy command based, or is the interface similar to the web-based platform?

ADD REPLYlink written 17 months ago by ChickenRNA50
1

The user interface is also web-based and from a usage perspective the same as what is found at http://usegalaxy.org. There is some very simple set-up with a few commands for a local but these are clearly documented. Cloudman also has some set-up and all is web-based. The links from the Choices wiki describe both.

I would suggest starting up a local quickly (should take less than 10 minutes) to give it a test drive.

ADD REPLYlink written 17 months ago by Jennifer Hillman Jackson23k
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