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
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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abhilashtripathi10 •
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