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DavidsonGroup / flexiplex

The Flexible Demultiplexer
https://davidsongroup.github.io/flexiplex/
MIT License
26 stars 2 forks source link

Degenerate bases #45

Closed cnk113 closed 2 days ago

cnk113 commented 4 months ago

Hi,

I was wondering if it was possible to allow a few degenerate bases in the primer sequences?

Best, Chang

olliecheng commented 4 months ago

Hi Chang, thanks for your interest in Flexiplex. There are a couple different ways to do this, depending on what you’re looking for. Flexiplex supports using IUPAC degenerate base symbols (such as Y, R etc) as well as “any base” using ? in both flanking sequences, if you know specifically where the degenerate/unknown bases are located in the wider primer sequence. Furthermore, Flexiplex allows for a more generic error-tolerant matching (using Levenshtein distance). To enable this for flanking sequences (such as primers), you can use the -f x parameter to enable an edit distance of x with the flanking sequences.

It is worth noting that by default, the flanking edit distance is 8. To disable this, use -f 0.

I hope that provides some clarity. If I haven’t addressed your question, an example sequence would be greatly appreciated!

Cheers Ollie