# FastQC read quality scores in general stats table **URL:** \ **Category:** Ask for help\ **Tags:** multiqc\ **Created:** [April 19, 2024, 2:37pm UTC](https://community.seqera.io/t/fastqc-read-quality-scores-in-general-stats-table/673 "2024-04-19T14:37:33Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![lskatz](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/lskatz/32/558_2.png) [@lskatz](https://community.seqera.io/u/lskatz)\ **Post date:** [April 19, 2024, 2:37pm UTC](https://community.seqera.io/t/fastqc-read-quality-scores-in-general-stats-table/673/1 "2024-04-19T14:37:33Z")
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. ![image](https://europe1.discourse-cdn.com/flex013/uploads/seqera/original/1X/d051ccc32016fa671a1a884e083a0c991b842500.png) Thank you for all your help! ---
**Author:** ![ewels](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ewels/32/1_2.png) [@ewels](https://community.seqera.io/u/ewels)\ **Post date:** [April 19, 2024, 3:35pm UTC](https://community.seqera.io/t/fastqc-read-quality-scores-in-general-stats-table/673/2 "2024-04-19T15:35:42Z")
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](https://github.com/MultiQC/MultiQC/issues/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](https://multiqc.info/docs/reports/customisation/#running-modules-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! Phil ---
**Author:** ![lskatz](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/lskatz/32/558_2.png) [@lskatz](https://community.seqera.io/u/lskatz)\ **Post date:** [April 19, 2024, 3:38pm UTC](https://community.seqera.io/t/fastqc-read-quality-scores-in-general-stats-table/673/3 "2024-04-19T15:38:48Z")
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. ---
**Author:** ![ewels](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ewels/32/1_2.png) [@ewels](https://community.seqera.io/u/ewels)\ **Post date:** [April 19, 2024, 5:57pm UTC](https://community.seqera.io/t/fastqc-read-quality-scores-in-general-stats-table/673/4 "2024-04-19T17:57:12Z")
Sounds good, would love to know how you get on. Thanks! ---
**Author:** ![ewels](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ewels/32/1_2.png) [@ewels](https://community.seqera.io/u/ewels)\ **Post date:** [April 19, 2024, 5:59pm UTC](https://community.seqera.io/t/fastqc-read-quality-scores-in-general-stats-table/673/5 "2024-04-19T17:59:10Z")
Note that there is a [7 year old pull request](https://github.com/MultiQC/MultiQC/pull/576) 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! Phil ---
**Author:** ![lskatz](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/lskatz/32/558_2.png) [@lskatz](https://community.seqera.io/u/lskatz)\ **Post date:** [April 19, 2024, 7:42pm UTC](https://community.seqera.io/t/fastqc-read-quality-scores-in-general-stats-table/673/6 "2024-04-19T19:42:16Z")
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 😃