I'm trying to design a suite of 10-15 microsat primers using NGS. I have the raw output files from the shotgun 454 sequencing (fna, qual and sff files). I could just ask the company that did the sequencing to design the primers but I really want to learn it myself. I've been reading extensively and trying various programs all of which seem to run on Python and require installation of about 5 different programs. So far I have managed to use FASTQC to check the raw files then NextGenWorkbench to trim them using the sff files. And then I get totally lost as to what to do next with QDD.......................I know it should be easy but I'm not great at software programs (better at field ecology!!) so any advice or pointers to webcasts that are simple to understand would be awesome!
Also, is it possible to multiplex primers in QDD?