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MultiQC - Mean quality score plot

I am new in RNA-seq analysis and I realized in my multiQC result I have two green parts in the Sequence Quality Histograms plot. As far as I know, the green part shows a good quality and usually for Phred scores higher than 25 it must be the case. I'm wondering what could be an explanation for this that I have two green parts in the plot?

enter image description here

multiqc
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updated by Phil Ewels Phil Ewels • written by Darya • Darya

Check the individual FastQC outputs and take a look whether something's off. That said, I think this is just a rendering issue. You could try re-running MultiQC if you haven't already.

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written by Dunois • Dunois

Thanks for your reply. I've already tried rerunning. I am going to check multiqc source code to see what's happening there.

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written by Darya • Darya

Thanks for your reply. No, I don't have this problem with the example reports. Unfortunately, I can't share my reports, as I'm working with confedential data but I made an issue in MultiQC repo.

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written by Darya • Darya

For future googlers: this was due to a very old version of MultiQC. Upgrading should solve the issue.

x-ref to the GitHub issue: ewels/MultiQC#1636

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written by Phil Ewels Phil Ewels

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