multiqc could not generate results

Question

[adR]

Hello all, I was running MultiQC in my current directory where my bam/fastqc files are located to generate some general statistic but could not get any result(No analysis results found. Cleaning up..)

I install the software and run it as follow

pip install multiqc
multiqc .

I would be happy if I get some comments

[Jautis]

Can you verify that it installed correctly, and post the full stdout?

Answer 1

[Phil Ewels]

MultiQC will ignore BAM files and on the off chance that FastQC was a typo for FastQ then it will ignore FastQ files as well. See https://multiqc.info/docs/#introduction

If you did run in a directory with FastQC reports (zip files or the .txt outputs) then please use -v to give the verbose log output and post that here.

Thanks!

Phil

[adR]

Dear Phil, so sorry the mistake was with me. I gave the fastq file instead of fastqc. Now it works. Thanks a lot. However, just for my understanding does multiQC have some post-alignment functionality? Best, adR

[Phil Ewels]

Nope, it does not. From the docs:

MultiQC is a reporting tool that parses summary statistics from results and log files generated by other bioinformatics tools. MultiQC doesn't run other tools for you - it's designed to be placed at the end of analysis pipelines or to be run manually when you've finished running your tools.