multiqc adding different file names and repeating same file twice

Question

[valizad2]

Hello all,

I have an issue with the output of multiqc. Everything looks good but for some of my outputs such as STAR alignment, for example, I get a graph that shows same file in two version of names, I checked and my files are named similarly in all of the folders. I used fastqc, STAR alignment and featureCount output as input. How can I attach a picture here?

[GenoMax]

How to add images to a Biostars post

If you think you have discovered a bug then post it on MultiQC GitHub site.

Answer 1

[valizad2]

I think the reason this was happening was because I had a subfolder inside the folders I shared with the multiqc, and it seems multiqc can actually access the files inside those as well. I deleted that folder and the output looks fine now. Thanks!