Previously I have been using FastQC to identify overrepresented sequences (adapters) to feed cutadapt tool for trimming.
Right now I have about 50 bam files (sequenced by Illumina) that need quality control including removing adapter seq, but I cannot go through FastQC individually to identify each "unique" adapters.
That said, I am wondering if it's possible to preload a long list of all known Illumina adapters into cutadapt? If so is there a simple text file that holds these adapters? If this is not the best method I am open to alternative solutions. Thank you guys for your help.