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Question: Using web based platform for analysis
1
gravatar for ChickenRNA
2.3 years ago by
ChickenRNA • 50
ChickenRNA • 50 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 • 580 views
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modified 2.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.3 years ago by ChickenRNA • 50
2
gravatar for Jennifer Hillman Jackson
2.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.3 years ago by ChickenRNA • 50
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 REPLY • link written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k
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