processAmplicons to match sequences 1 or 2 bases shorter than guides?
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sdalin • 0
@sdalin-15843
Last seen 6.1 years ago

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!

processamplicons edgeR • 800 views
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