Entering edit mode
2.2 years ago
Darya
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0
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?
Check the individual
FastQCoutputs and take a look whether something's off. That said, I think this is just a rendering issue. You could try re-runningMultiQCif you haven't already.Thanks for your reply. I've already tried rerunning. I am going to check multiqc source code to see what's happening there.
I'm pretty sure that you won't find anything in the source. Do you see the same thing when you view an example report on the MultiQC website, such as https://multiqc.info/examples/rna-seq/multiqc_report.html#fastqc_per_base_sequence_quality ?
If not, please make an issue on the MultiQC repo and attach your HTML report and a FastQC report that causes this and I can take a look and see if I can replicate it my end.
Phil
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.
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