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rraadd88 / beditor

A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated Base Editing, and much more
GNU General Public License v3.0
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positive control #8

Closed bioinfo4321 closed 5 years ago

bioinfo4321 commented 5 years ago

Hi, this is not really an issue but a question. My understanding was positive control guides would introduce non-sense mutations. However, in a run i did, it is returning a number of guides only a fraction of which are introducing non-sense mutations, rest are just regular substitutions. Is there any reason that may be happening.

Also, what would is the purpose of option "keep_mutation_nonsense" in cfg.

Thank you.

rraadd88 commented 5 years ago

Hi @bioinfo4321 ,

keep_mutation_nonsense option will not filter out the non-sense mutations. This option is applicable when only the position of the mutation is provided as an input. (In such a case, beditor scans all the possible mutations at that position. If you wish to keep the non-sense mutations in the output, you'd need to choose keep_mutation_nonsense.

As with the run of yours that produced only fraction of the gRNAs that were non-sense mutations, I'd say the design of the gRNA would depend on compatibility of the base editor you are using with the codon substitutions allowed (termed as "editibility" in the manuscript). Other major reason would be sequence context, for instance, if there are no PAM sites nearby, beditor won't be able to make any gRNAs.

I hope that helps. Thank you for the question. (I will include a blurb about this in the documentation.)

rraadd88 commented 5 years ago

[Closing the issue now ]