icbi-lab / duurland2021_paper

Single-cell analysis for Duurland et al.

Single-cell data analysis for Duurland et al. (2021)

This repository contains a nextflow pipeline that reproduces the entire single-cell RNA-seq data analysis from our paper.

The data analysis reports generated by this pipeline are available here: https://icbi-lab.github.io/duurland2021_paper.

How to run

1. Acquire the data

Please follow the data sharing statement in the paper.

Deposit the cellranger files in the data directory. The files must follow the following structure:

data/cellranger/{SAMPLE}_GEX/outs/raw_feature_bc_matrix.h5

Gene expression data from three publicly available Smart-seq2 datasets are available on the release page and will be downloaded automatically by the pipeline.

2. Run the pipeline

Prerequisites:

• Nextflow
• Singularity

Clone the repository:

git clone https://github.com/icbi-lab/duurland2021_paper.git

Start the pipeline:

nextflow run main.nf

Nextflow will automatically download the required singularity containers and run the analysis.

• The reports will be stored in the deploy folder.
• All (intermediate) results are stored in the results folder.

Citation

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