I’m trying to parse stats from featureCounts in multiqc version 1.30. The problem is the General Statistics table only shows the %Assigned, not the total number of assigned reads. I can see that in the featureCounts specific plot below, so it has that data, but I want to be able to see the overall violin plot with outliers for total number of reads.
Is there a way to force that specific statistic to appear in the General Statistics table? Or a more general way to choose between absolute numbers and percentages in the general statistics table.
Can I ask why you need this in General Stats? The data is available in several places for downstream analysis already if that’s what you’re thinking. Otherwise the question of which values to put into General Stats is quite subjective and basically lies with the MultiQC developer (me ).
You can customise this behaviour by running MultiQC in a script, or passing featureCounts reads back into the report via Custom Content. Neither is very clean, but those are the general escape hatches that let you do whatever you want if the default MultiQC behaviour isn’t working how you want.
I have wondered about a general config mechanism to allow arbitrary module data to be put into general stats, but it’s very difficult to generalise well.
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