I'm trying to mine SSR from my assembled sequences and design primer pairs for them.
I used MISA for SSR mining. As the manual stated, I supposed to get 2 output files: in .misa format and .statistics format. However, what I got are a .statistics file and more than 100,000 .gff files! That made me shocked.
At first, I planned to use a .misa output for primer design in Primer3. But when I encounter with a ton of .gff files, I really don't know what to do next. I already searched it if anyone has the same problem but no, others seem to get a .misa file from MISA.
Can I use those .gff with Primer3? Do I have to input a .gff file at a time? (so if I want to design primer for all SSR, I have to run at least 100,000 times) Did anyone have the same problem as mine? How did you solve it? Or anyone else could run it successfully without a problem?
Thank you, Putita