Hi All,
I notice in my FastQC results from several paired end Illumina sequencing runs that the adapter-index primer is an overrepresented sequence in the R1 fastq file only, and not in the R2 fastq file. Is that because the FastQC is searching with the complement Adapter sequence which would be the reverse complement in R2? or is it that there are really no Adapter-Index sequences in R2?
Best,
Jos
•
written
by
landrjos •
1 answer
In normal case, if R1 has adapters, R2 should also have adapters.
But there is an exception: the quality of R2 is much worse than R1 so have too many sequencing errors in the tails of R2. Then, due to the sequencing errors are relative random, the over representation will be reduced.
I suggest to preprocess your data and cut the adapters with fastp: https://github.com/OpenGene/fastp
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FastQC only looks at a fraction of the data when it checks over-represented sequences. If you see adapters in R1 then they are bound to be there in R2. You should scan and trim the data.