Tutorial:Video: RNA-Seq Alignment and Visualization using Galaxy and IGB

Question

[Nowlan Freese]

"Focus on a Feature: RNA-Seq Alignment and Visualization using Galaxy and IGB."

This Focus on a Feature has finished. You can find the recording here:

https://www.youtube.com/watch?v=LsmSzxh2RQ8

To follow along, you can find the data I used in Galaxy here.

Previous Focus on a Feature recordings can be found here.

Program:

1. Introduction to Galaxy
2. Finding and loading data sets from the Sequence Read Archive
3. Quality checking and grooming of NGS data.
4. Aligning NGS RNA-Seq data.
5. Visualizing RNA-Seq alignments in IGB

Integrated Genome Browser (IGB)

IGB provides an advanced, highly customizable environment for exploring and analyzing large-scale genomic data sets. Using IGB you can visually analyze RNA-Seq, ChIP-Seq, and many other genomic projects. The best part of all is that IGB can be used to produce publication quality images from genome scale data sets, and is provided FREE.

If you have questions or need assistance, contact us at:

Nowlan Freese: [e-mail]

Ann Loraine: [e-mail]

To download and start IGB, go to bioviz.org and select the "Download Now" link. Once IGB starts, choose Help / Tutorials for a quick introduction to IGB.

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Answer 1

[CikLa]

Hi,

Good tool to use! Thanks for the information. Just one question, can IGB be integrated into Galaxy?

[Nowlan Freese]

Hi CikAlal,

Great question! IGB is fully integrated into Galaxy. Once you've generated a file in Galaxy the option to "display in IGB" will appear. Clicking on the link will automatically load the data into IGB (you will need to have IGB running).