I'm a beginner in RNAseq analysis (Illumina, PE reads). In FastQC, I got a failure on "Per base N content" towards the 3' end (95-99bp). I would expect quality score to drop here but the scores are above 32. Is this normal?
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Can you post the plot? It is possible that a fraction (above the threshold) of the reads have N's in those positions. Those could be trimmed out. -
RNAseq fastqc - Failed "Per base N content"
Thanks GenoMax for your prompt feedback.
Here you have the plots.Comment
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That is what I had thought (looks good otherwise). A bit of trimming should get rid of the N's. Most aligners will also soft-clip those N's if they are at the end of the reads.Comment
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Nothing to worry about then? Thanks!Comment
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Nope. Go ahead and trim the reads (lots of other threads on trimming programs).
Re-check FastQC afterwards and that "fail" should be gone.Comment
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