Design qpcr primers

Question

[sbchua.1990]

Hi, I did RNA-seq experiment and now I wish to validate my data using real time qPCR.

Any suggestion for softwares and pipeline for primers design? How to design primers that span exon-exon junction?

Answer 1

[James Ashmore]

If you need to design a small number of primers then use an online web tool such as Primer-BLAST, however if you have need to design hundreds then it's probably easier creating your own primer design pipeline from various open source tools. Right now, I'm using the command-line version of primer3 to design my primers, and then using primersearch to make sure they are unique.