I'm currently working on mammal genomes. I had received Illumina NGS data and decided to use QDD (on Windows) to fish out microsatellites for PCR primer design. I've encountered some problems and hopefully someone can help me up here.
By following the instructions in http://net.imbe.fr/~emeglecz/qdd_installation.html, I've downloaded Active Perl, BLAST+, ClustalW and Primer3. For Primer3, should I downloaded version 2.3.7 (the C code), version 4.0.0 (Web Interfaces - Primer3 Web) or 2.3.6 (Web Interfaces - Primer3Plus)?
Can I use the raw data from NGS (paired ends reads, 1GB) as the input file for Pipe1 in QDD?
I've tried the above and my laptop is still working on Pipe2 after 12 hours. How long will Pipe2 and Pipe 3 take for a sample size 1GB?
Anyone has a detail workflow for using QDD on Windows to design PCR primers?
Thank you in advance for helping.