`addSpacerAlignments` maximum `n_mismatches` query

crisprVerse / crisprDesign

Comprehensive design of CRISPR gRNAs for nucleases and base editors

MIT License

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`addSpacerAlignments` maximum `n_mismatches` query #16

Closed MatthewPace98 closed 1 year ago

MatthewPace98 commented 1 year ago

Our team has detected some off-target editing in vitro in regions with 4 or 5 mismatches when aligned to the gRNA, and we would like to design guides with this in mind. I understand that increasing the number of allowed mismatches would exponentially increase the computational demand, but I think it would be useful to attempt addSpacerAlignments with n_mismatches> 3. Could this be implemented, please?

Jfortin1 commented 1 year ago

This is possible using bwa instead of bowtie as the aligner