FastQC read quality scores in general stats table

Hi, I want to have quality scores on the general statistics line for my Illumina raw read files. I wanted to have a Q score for each R1 and R2. How would I do that best?

Right now, I have it with FastQC, but R1 and R2 are forming new “samples” on the general statistics table like so.


Thank you for all your help!

This is a common request and it’s unfortunately not a simple one. There is a very old issue with ideas to tackle it in #542 which we hope to work on soon.

In the mean time, I think that you might be able to run the FastQC module multiple times and filter by file path, then use sample name cleaning to get everything to line up on one line. But then all fields will be duplicated.

Otherwise you can pre-process the data and show it via Custom Content.

Or you can write a MultiQC plugin to customise the parsed data before rendering the report. Soon you’ll be able to run MultiQC in Python scripts as a library and do the same thing without needing a plugin.

Hopefully some pointers there, sorry that there isn’t an easier answer for now!


Thank you! I think with my previous question about adding custom fields to the general stats table, I might be able to hack this one. I’ll also look into the solution where we might be able to run it multiple times. If that works, I’ll report back.

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Sounds good, would love to know how you get on. Thanks!

Note that there is a 7 year old pull request to add a new feature for the issue linked above, which @vlad.savelyev has been recently working on. It’s still very much under active development, but if you fancy having a play with the dev-code on that PR and providing feedback it would be welcome!


I wish I could help! I’m not very good in Python though.

It turns out that the fix did work to split R1 and R2! But in the end, I couldn’t really figure out how to integrate it into the general stats table per sample. Therefore, I decided to keep the complex output. Since I can’t code in Python too well, I’ll stay on the production branch but I look forward to that PR :smiley:

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