From 4938549d65d53c79d53cd1d3908294102e4968d9 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Mon, 6 Mar 2023 10:41:32 +0100 Subject: [PATCH] Clarify some documentation --- docs/output.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/output.md b/docs/output.md index 0a2e2d0..0620292 100644 --- a/docs/output.md +++ b/docs/output.md @@ -35,19 +35,21 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution -### FastQC or falco +### FastQC or Falco
Output files - `fastqc/` - - `*_fastqc.html`: FastQC report containing quality metrics. - - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. + - `*_fastqc.html`: FastQC or Falco report containing quality metrics. + - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images (FastQC only).
[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). +If preprocessing is turned on, nf-core/taxprofiler runs FastQC/Falco twice -once before and once after adapter removal/read merging, to allow evaluation of the performance of these preprocessing steps. Note in the General Stats table, the columns of these two instances of FastQC/Falco are placed next to each other to make it easier to evaluate. However, the columns of the actual preprocessing steps (e.g., fastp or AdapterRemoval) will be displayed _after_ the two FastQC/Falco columns, even if they were run 'between' the two FastQC/Falco jobs in the pipeline itself. + > ℹ️ Falco produces identical output to FastQC but in the `falco/` directory. ![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) @@ -56,8 +58,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d ![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) -> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. - ### fastp [fastp](https://github.com/OpenGene/fastp) is a FASTQ pre-processing tool for quality control, trimmming of adapters, quality filtering and other features.