# Quality Control Start Here! multQC issue and guidance?

**URL:** https://help.galaxyproject.org/t/quality-control-start-here-multqc-issue-and-guidance/14914
**Category:** Resources
**Tags:** fastqc, collection-shape, collections, resources, troubleshooting, multiqc, quality-control
**Created:** [March 3, 2025, 4:09pm UTC](https://help.galaxyproject.org/t/quality-control-start-here-multqc-issue-and-guidance/14914 "2025-03-03T16:09:54Z")
**Posts on this page:** 1
**Showing post:** 2

<div class="post-metadata">

### Author: ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [March 3, 2025, 5:47pm UTC](https://help.galaxyproject.org/t/quality-control-start-here-multqc-issue-and-guidance/14914/2 "2025-03-03T17:47:50Z")

</div>

Hi @Martyn

The immediate issue is that the input collection is in a nested “paired list” shape. **MultiQC** is expecting a simple “list” collection.

#### How to get from the SRA “paired list” output collection shape to a simple “list” collection shape?

Use the `Faster Download and Extract Reads in FASTQ format from NCBI SRA` tool

Then, when running `FastQC` on a paired end collection, it is useful to first apply the `Collection Operations -> Flatten Collection` tool. This assigns a unique sample identifier to each end of the pair – giving the sequences a distinct collection identifier. `MultiQC` will then provide the results for each sequence end, and summarize correctly.

Single dataset QA example

- [Hands-on: Quality Control / Quality Control / Sequence analysis](https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html)

Multiple paired end dataset QA example

- [Hands-on: Reference-based RNA-Seq data analysis / Reference-based RNA-Seq data analysis / Transcriptomics](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html) (see the initial steps)
- More examples → [Galaxy Training!](https://training.galaxyproject.org/training-material/by-tool/iuc/sra_tools/fasterq_dump.html)

A demonstration is in the **Quality Control Q20-L20** public workflow.  
How to find it →

> [@Trimming with different parameters/tools give vastly different end results.](https://help.galaxyproject.org/t/trimming-with-different-parameters-tools-give-vastly-different-end-results/14815/2):
>
> - Search here [GalaxyProject.org](http://GalaxyProject.org) → [GTN Pan-Galactic Workflow Search](https://training.galaxyproject.org/training-material/workflows/list)
> - With the term `Quality Control Q20-L20`

**What to do**

1. Run the `Flatten Collection` tool on the output from `Faster Download and Extract Reads in FASTQ`
2. Run `FastQC` on the result (a simple “list” collection format)
3. Run `MultiQC` on the result.

Or, you can try the workflow. You can customize the trimming step, or ignore it, or remove that step in your copy of the workflow.

Please let us know if this helps or not, and we can follow up more! 🙂

---

_[View the full topic](https://help.galaxyproject.org/t/quality-control-start-here-multqc-issue-and-guidance/14914)._