fastp results, per base content
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6 months ago
minifoog ▴ 10

Should I be concerned with the per base ratio content despite having good quality scoring on every base position? Per base content

Quality score

fastp quality perbasecontent ubuntu • 384 views
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Going to leave a link for a blog post FastQC developers have on this very topic for future visitors to this thread. As Antonio said below nothing to worry about.

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6 months ago

If you are concerned about the bias observed in the first 9 bases, that is absolutely normal in Illumina sequencing when a mechanical method of breaking the DNA to get the shotgun fragments in used. It turn out that DNA is more fragile in some sequences, and this is why you see it

It does not affect your analysis

I see in the second graphic a high quality even at the end

If you don't see GC bias and the presence of adapters and/or a high level of duplicated or overrepresented sequences, I would say that sequencing went just fine and you do not require to filter. You did not mention whether DNA or RNA is used

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