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eclarke / swga

Select primer sets for selective whole genome amplification (SWGA)
GNU General Public License v3.0
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Parameters for similar genomes #40

Open Niyo2fine opened 6 years ago

Niyo2fine commented 6 years ago

Hi, I am working with genomes of two co-infecting similar species as foreground and background genomes. So far I have not successfully obtained any primer sets at all, even after adjusting some of the parameters. I have had between 125 -196 primers marked as active after filtering but nothing comes up with the swga find_sets command. I was wondering if there are specific parameters I can adjust and how stringent/relaxed can I go when the genomes are similar?

eclarke commented 6 years ago

I'd suggest modifying the min_bg_bind_dist and max_fg_bind_dist parameters to be smaller and larger, respectively, in the find_sets command. There's a status bar that appears when you run find_sets showing the smallest average distance found so far in the foreground as it checks sets; this number can be used to adjust the max_fg_bind_dist.

jan36 commented 6 years ago

hi, I have the same problem like Niyo2fine. I have had a lot of primers but when I run find_sets with suggested modifications following massage appear: "No compatible primers. Try relaxing your parameters".

jan36 commented 6 years ago

Any suggestion what parameters I should relax please?