It is a naive question, but I am still new :)
How can I check if there is remaining short adapters in the reads if FastQC adapter content shows no adapters? When I search the original reads for "AGATCGGAAGAGC" , I found plenty. But when I search the reads for this sequence after trimgalore/cutadapt, there is nothing. If there is small subsequence of this sequence (presumably remaining of the adapters), how can I guarantee they are not a part of native sequence. So, how can I say, there is a remainings of the adapters?