When I have short insert size where it is possible that the adapters run into the reads. I trimmed the adapters using cutadapt/trimgalore. FastQC reports regarding adapter contents show no adapters. Is this sufficient or I do need to do more aggressive adapter trimming? Keeping in mind that we still have around 70% alignment with Tophat or 75% mapping rate with Salmon. My professor suggest that I still have adapters in the reads. Is it possible if FASTQC report no adapters. So how can I know how much more trimming is yet needed?