The software I am using for demultiplexing allows to specify adapters in the samplesheet so that the adapters can be trimmed. However, I noticed that when I did multiqc on my fastq files there are adapters left. I am including some examples below. In this example the adapter content is pretty low but I have had other samples with 3-7% adapters on the multiqc file.
When I specify the adapter exactly as Illumina says on their manual the adapter can reach up to 0.74%. The software also allows for automatic detection of the adapters. When I use that the adapter sequence that is picked up is the illumina adapter sequence+ 5 more bases. When I use that for adapter trimming multiqc says: No samples found with any adapter contamination > 0.1%
I wanted to know what would be the more appropriate way to trim the adapters? Would the extra 5 bases cause an issue?