I usually remove adapters prior to mapping. I wrote a program called SeqPrep to do this. More reads will map when you trim before mapping, also my program uses the overlap between the pair of reads as well as matches to the adapter (you are doing pairs, right?). That said if you are not doing pairs of reads, do not use SeqPrep, it is only for paired reads. If you are using single ended reads any tool that does adapter trimming (think there is one in GATK as well as Picard's CleanSam). The lab I used to be in used Trimmomatic for adapter trimming. There are a ton of programs though that will work reasonably well on single-ended reads if that is what you have.