I got my samples sequenced from a commercial facility. They used the following adapter sequences for sequencing
|Sample ID|Index i7|Index i5|
I am confused with the nomenclature of adapters. I am trying to use the Cutadapt tool in galaxy, and I am not sure out of the given adapter sequences which are 3’(End) adapters, 5’(Front) adapters, or 5’ or 3’ (Anywhere) Adapters. I also tried using the trimmomatic tool but I am not sure if I should use the TruSeq2 (pair ended) or TruSeq3 (pair ended). Could anyone please guide me through this so that I can start my data analysis? Thank you.