I'm working on using processAmplicons to map my reads to my library's guides.  After talking to my department's bioinformatics core, they suggested allowing up to 2 mismatches, as well as 'truncated' matches, ie, the guides are 20 bases long, so an 18 or 19 base match.  Is there a way to map truncated matches like this with edgeR/processAmplicons? I am using the shiftingBase option, but its not clear to me if that would provide this type of partial match I am referring to.

Thanks!