QClus: a droplet filtering algorithm for enhanced snRNA-seq data quality in challenging samples
Single-nuclei RNA sequencing remains a challenge for many human tissues, as incomplete removal of background signal masks cell-type-specific signals and interferes with downstream analyses. Here, we present Quality Clustering (QClus), a droplet filtering algorithm targeted toward challenging samples. QClus uses additional metrics, such as cell-type-specific marker gene expression, to cluster nuclei and filter empty and highly contaminated droplets, providing reliable filtering of samples with varying number of nuclei and contamination levels. In a benchmarking analysis against seven alternative methods across six datasets, consisting of 252 samples and over 1.9 million nuclei, QClus achieved the highest quality in the greatest number of samples over all evaluated quality metrics and recorded no processing failures, while robustly retaining numbers of nuclei within the expected range. QClus combines high quality, automation and robustness with flexibility and user-adjustability, catering to diverse experimental needs and datasets.
Authors
- Suvi Linna-Kuosmanen (ORCID: https://orcid.org/0000-0002-3278-2727)
- Kristiina Harju
- Minna Unelma Kaikkonen (ORCID: https://orcid.org/0000-0001-6294-0979)
- Eloi Schmauch (ORCID: https://orcid.org/0000-0002-2123-8777)
- Juha E.K. Hartikainen (ORCID: https://orcid.org/0000-0003-0847-107X)
- Hannu Kokki (ORCID: https://orcid.org/0000-0001-5922-7195)
- Jari Halonen (ORCID: https://orcid.org/0000-0003-3878-1546)
- Johannes Ojanen
- Jarmo Gunn (ORCID: https://orcid.org/0000-0002-6996-0726)
- Juho Jalkanen (ORCID: https://orcid.org/0000-0002-1693-8293)
- Maija Hollmén (ORCID: https://orcid.org/0000-0002-3250-7653)
- Tuomas Kiviniemi (ORCID: https://orcid.org/0000-0002-0908-3741)
- Pasi Tavi (ORCID: https://orcid.org/0000-0003-2563-3616)
- Manolis Kellis (ORCID: https://orcid.org/0000-0001-7113-9630)
- Kyriakitsa Galani
Institutions
- Broad Institute (US)
- Vassar College (US)
- Brigham and Women's Hospital (US)
- Harvard University (US)
- University of Turku (FI)
- University of Eastern Finland (FI)
- Turku University Hospital (FI)
- Kuopio University Hospital (FI)
- Massachusetts Institute of Technology (US)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2024-11-04
- DOI
- https://doi.org/10.1093/nar/gkae1145
- Citations
- 2
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.47
Funders
- Foundation for Cardiovascular Research
- Itä-Suomen Yliopisto
- Yrjö Jahnssonin Säätiö
- Maud Kuistilan Muistosäätiö
- Aarne Koskelon Säätiö
- Academy of Finland
- Suomen Kulttuurirahasto
- Sydäntutkimussäätiö
- Orionin Tutkimussäätiö
- Saastamoisen säätiö