This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Tutorial: Video: Alternative Splicing and Primer Design

"Focus on a Feature: Alternative Splicing and Primer Design"

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

https://www.youtube.com/watch?v=1LUszUX2wuA

Program:

  1. Introduction to IGB
  2. Loading data sets
  3. Navigating through a genome
  4. Viewing alternative splicing
  5. Designing and visualizing primers

Integrated Genome Browser (IGB)

IGB is a highly interactive, fast, and easy to use desktop genome browser, which is used to view and interact with sequence data from reference genomes, gene models, and alignments. Common data sets include RNA-Seq, ChIP-Seq, and other genome-scale projects. IGB can be used to produce publication quality images from genome scale data sets, and is provided FREE. IGB has a dedicated support staff and is continuously updated with new functionality.

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

Nowlan Freese nfreese@uncc.edu

Ann Loraine aloraine@uncc.edu

*Please test-run IGB before the tutorial. 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.

Please share this with students and colleagues

rna-seq igb
• 5,467 views • link
updated by Ram Ram • written by Nowlan Freese Nowlan Freese

1 answer

Hi Nowlan Freese,

Is it possible to use IGB to design primers for alternative splicing events? The following page is empty: https://wiki.transvar.org/display/igbman/Primer+Design

Best,
Pengcheng Yang

• 0 views • link
updated by Ram Ram • written by pengchy pengchy

Hi Pengcheng Yang,

There is currently no way to design primers from within IGB. My advice would be to use IGB to identify regions of alternative splicing, and then use primer 3 to pick primers.

1) Identify alternative splicing event of interest in IGB.

2) Copy the DNA sequence directly from IGB and paste it in primer 3 (http://biotools.umassmed.edu/bioapps/primer3_www.cgi).

3) Use primer 3 to pick primers.

4) Visualize the primers in IGB using the Advanced Search tab to verify that they capture the alternative splicing event.

We're in the process of greatly expanding support for user developed plug-ins in IGB. The page on primer design in the IGB user's guide is a placeholder at the moment, but is a feature we would like to add in the future.

Nowlan

• 0 views • link
updated by Ram Ram • written by Nowlan Freese Nowlan Freese

Hi Nowla,

Thanks for your reply. It will be useful to visualize the primers on alternative splicing exons using IGB.

Pengcheng

• 0 views • link
written by pengchy pengchy

Log in to answer this question.

More posts like this