I have been advised by a colleague to get a pool of cDNA serial dilution and do the primer efficiency test. I have 16 different genes from 2 species of oilseed rape (Brassica napus and Brassica napus) and a fungus Pyrenopeziza brassicae. I am confused do I use the same thermal cycles for all? How do I determine what thermal cycles I have to use?
The serial dilution is the way to go. Fortunately, you may need very similar dilutions between species.
Regarding of the cycles, look first at the bibliography to see if there is a standard program for them (for example, I used the same program as other researchers used for GFP and it worked). Usually the machine would suggest its own thermal cycles, and you only need to adjust the annealing step (at least in my machine), the rest of the steps are pretty standard.
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