If you give fastqc 2 adapters to search:
adapter1: AATTAATTAATT (width = 12)
adapter2: AAATTTGGGAAAAAATTTGGGAAA (width=24=max_adapter_size)
Let us say all reads in the fastq file are 51nt long:
Fastqc will only search for adapters starting from position 1 to (51-max_adapter_size = 27), i.e. all reads where adapter started at position > 27nt, would never search for adapter1, (because the start position of adapter is too high relative to adapter2) !
This scanning up until only 27 makes sense for adapter 2, but it should in no way affect the search for adapter1!
If fastqc wants to use a "maximum adapter size based search", this must clearly be specified in the documentation and the --adapter argument, as we have used it for years without understanding why it failed in many cases to detect adapters.
If you give fastqc 2 adapters to search:
adapter1: AATTAATTAATT (width = 12)
adapter2: AAATTTGGGAAAAAATTTGGGAAA (width=24=max_adapter_size)
Let us say all reads in the fastq file are 51nt long:
Fastqc will only search for adapters starting from position 1 to (51-max_adapter_size = 27), i.e. all reads where adapter started at position > 27nt, would never search for adapter1, (because the start position of adapter is too high relative to adapter2) !
This scanning up until only 27 makes sense for adapter 2, but it should in no way affect the search for adapter1!
If fastqc wants to use a "maximum adapter size based search", this must clearly be specified in the documentation and the --adapter argument, as we have used it for years without understanding why it failed in many cases to detect adapters.