I am having trouble interpreting some of my multiqc plots for my quality assessment of my fastq files (E. coli samples). I have the following chart which shows good results for the per sequence quality scores plot (all samples pass). See figure below.
However, when I look at the sequence quality histograms showing the mean quality scores for each bp, I have the majority of my samples "failing". See figure below.
Can anyone help explain what is going on here?
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gt •
1 answer
when I look at the sequence quality histograms showing the mean quality scores for each bp, I have the majority of my samples "failing"
I am not sure why MultiQC is labeling your samples in Red in second plot.
Graph 1 shows mean sequence quality across the entire read in your dataset and that value is > 35 (really good).
Graph 2 is mean quality score at each base position in these reads. Again > Q35 across almost entire read (save a few bases at the beginning).
That dip at the beginning is likely because of this considering you have a RNAseq dataset.
I suspect that if you look at the underlying FastQC report the box plots will show a wide range in read qualities. From the FastQC help:
This module will raise a failure if the lower quartile for any base is less than 5 or if the median for any base is less than 20.
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