What to enter as adapter sequence of Cutadapt tool?

1

I’m having trouble entering the adapter sequences in the CutAdapt tool in Galaxy. According to the Illumina Adapter Sequences sheet , the following sequences are used for TruSeq adapter trimming:

Read 1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

Read 2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

However, the instructions below the Cutadapt tool in Galaxy suggest entering a different Read 2 sequence for TruSeq adapter trimming:

Read 2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT

I’m confused about how this Read 2 sequence is obtained and why it’s different from the one provided in the Illumina Adapter Sequences sheet for paired-end data. Can I use the Read 2 sequence provided in the Illumina Adapter Sequences sheet (AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) instead?

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2

Hi @Maryam_Momeni
Maybe try both options on a single sample and check the results with FastQC, especially the contamination section.
Hope that helps.
Kind regards,
Igor

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