Problem with recognizing adapters while using Cutadapt or Trimmomatic

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.

Hi @abhilash719,
i7 index adapter corresponds to the 3’ adapter and i5 index adapter to 5’ adapter. Regarding the ILLUMINACLIP options, it depends on the technology used; according to the Trimmomatic manual TrueSeq2 is used in samples generated by GAII systems, while TrueSeq3 should be used when the samples have been generated by HiSeq and MiSeq machines.

Thank you so much, @gallardoalba.

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