Introduction

nf-core/stableexpression is a bioinformatics pipeline that aims at finding the most stable genes among a single or multiple public / local count datasets. It takes as input a species name (mandatory), keywords for expression atlas search (optional) and / or a CSV input file listing local raw / normalized count datasets (optional). A typical usage is to find the most suitable qPCR housekeeping genes for a specific species (and optionally specific conditions).

Pipeline summary

1. Get Expression Atlas accessions corresponding to the provided species (and optionally keywords) (Expression Atlas; optional)
2. Download Expression Atlas data (Expression Atlas; optional)
3. Normalize raw data (using DESeq2 or EdgeR)
4. Map gene IDS to Ensembl IDS for standardisation among datasets (g:Profiler)
5. Compute gene variation coefficients and get the most stable genes

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet listing the different count datasets:

datasets.csv:

counts,design,normalized
path/to/normalized.counts.csv,path/to/normalized.design.csv,true
path/to/raw.counts.csv,path/to/raw.design.csv,false

Make sure to format your datasets properly:

counts.csv:

,sample_A,sample_B,sample_C
gene_1,1,2,3
gene_2,1,2,3
...

design.csv:

sample,condition
sample_A,condition_1
sample_B,condition_2
...

Now you can tun the pipeline as follows:

nextflow run nf-core/stableexpression \
  -profile docker \
  --species <SPECIES> \
  --eatlas_accessions <ACCESSIONS> \
  --eatlas_keywords <KEYWORDS> \
  --datasets ./datasets.csv \
  --outdir ./results

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/stableexpression was originally written by Olivier Coen.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #stableexpression channel (you can join with this invite).

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.