Problem with recognizing adapters while using Cutadapt or Trimmomatic

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1

I got my samples sequenced from a commercial facility. They used the following adapter sequences for sequencing
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|Sample ID|Index i7|Index i5|
|S0A|GTTCTTCTGT|CCAAGGTATT|
|S0B|CCAAGGTATT|GTTCTTCTGT|
|S0C|TGTGGAGAGG|AACGAACCGG|
|S5A|TTCCTTGAGG|TGCTGTCTTA|
|S5B|GTTAATTGCG|GAGGAGATAA|
|S5C|GAGGAGATAA|GTTAATTGCG|
|S15A|GTTCCTCATT|AATGTCGGTT|
|S15B|AATGTCGGTT|GTTCCTCATT|
|S15C|TTGACAGGTA|TGGTGGTTGT|

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.

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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.

3

Thank you so much, @gallardoalba.

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