Wildcards in Adapters

[Kendell Clement]

Is there way to have wildcards in the specified adapters? For example, an adapter with sequence "CCNNCC" would match any bases for the "N" bases.

[Erik Aronesty]

N's or even X's do work as wildcards, yes.  They count as "always mismatch".   Then just up your mismatch count.

CCXXCC would never match the XX, then you up the allowable mismatch count by 2.