N content - Sequence Quality
Hello,
I am working with WGS data sequenced on a NovaSeq X+. I used Fastp for preprocessing, including applying N-base filtering. However, upon reviewing the MultiQC report, I noticed high N-content in Read 1 both before and after preprocessing with Fastp.
This is the plot generated by MultiQC for Read 1 after filtering. Is this level of N-content alarming? How should I proceed to address this issue ?
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How many bases does do those N's cover (one or more than one)? It is possible that an aligner will be able to soft-clip or work around that region when aligning the data you have. You may want to hard-trim the first 10 bases. SInce you have plenty long reads, losing first10-15 bases should not affect alignment.