Single cell RNA-seq preprocessing: Prepare data

Prepare your single cell RNA-seq data for the Preprocessing phase of the Experiment roadmap

Prepare data is the first preprocessing step in the Preprocessing phase of the Experiment roadmap. The Prepare data step is automatically done following successful completion of the single cell RNA-seq pipeline (1, 2) and requires no user input.

The Prepare data step gathers the Cell Ranger output from the single cell RNA-seq pipeline to collect the gene counts and prepare cell-level metadata in order to create an initial, raw Seurat (3) object in the Initialize workflow preprocess.

The Prepare data step also computes useful metrics (e.g. number of doublets/multiplets), which are available for assessment during later stages of the Preprocessing phase.

In the Prepare data modal, you will find an Instructions & Tips section for more information about the preprocess, a Methods section, and quick reference to your sample-level metadata table.

References

1. Ewels et al. The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology (2020). doi: 10.1038/s41587-020-0439-x

2. nf-core/scrnaseq. doi: 10.5281/zenodo.3568187

3. Hao and Hao et al. Integrated analysis of multimodal single-cell data. Cell (2021). doi: 10.1016/j.cell.2021.04.048