I am testing a new software that is supposed to automatically detect adapters and remove them. I am using the adapters shown here: https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/TruSeq/UDIndexes.htm
I run the demultiplexing+ adapter trimming and the software does not see to recognize this adapter. However, when I check the data with fastqc I notice that it does not seem to find adapters on the adapter content plot. Does anyone know if fastqc can detect the adapters from the link above? I have not been able to find which adapters fastqc can detect.