Strange adapters question before running QIIME2

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1

Hi all! I've encountered a strange result with the quality control analysis.
Using FastQC, it is reported that in a small percentage of the reads (~4-7%) of all samples, there is an adapter sequence (Illumina universal adapter) located in the center of the reads.

adapter_raw
adapter_raw1513×691 19.4 KB
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What i usually do is merging the paired-end reads using PEAR and then perform the trimming step using fastp. What's weirder is that the adapter sequence changes (Illumina adapter small RNA 3') after the trimming!

adapter_merged_trimmed
adapter_merged_trimmed1511×701 15.8 KB

Hope you guys can help me find out the reason to this. Thank you!

2

Hi @Phoe

This is unusual but intriguing all the same. Can you post the settings you used for FastP?
The important parameters to look at are:

Parameters Information

--detect_adapte_for_pe (makes sure adapter detection for PE reads)

--cut_by_quality3 & --cut_by_quality5 which will trim the bases at both ends based on quality.

--adapter_sequence & --adapter_sequence_r2 where you can specify the adapter sequences (You mentioned Illumina universal adapters)

I think these are the sequences to use in the final parameter:

Adapter read 1 sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

Adapter read 2 sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

Hope that helps!