Journal
GENOME BIOLOGY
Volume 22, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-021-02469-x
Keywords
Multiplets; Doublets; Single nucleus ATAC-seq; snATAC-seq
Funding
- PhRMA Foundation
- National Institute of General Medical Sciences (NIGMS) [GM124922]
- Department of Defense [W81XWH-18-0401]
- American Diabetes Association [1-18-ACE-15]
- National Cancer Institute [F31CA257349]
- National Institute on Aging (NIA) [R01AG052608]
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Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging, but AMULET shows high precision and recall compared to alternatives, especially when a certain read depth of 25K median valid reads per nucleus is achieved.
Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned reads across the genome to effectively detect multiplets. We evaluate the method by generating snATAC-seq data in the human blood and pancreatic islet samples. AMULET has high precision, estimated via donor-based multiplexing, and high recall, estimated via simulated multiplets, compared to alternatives and identifies multiplets most effectively when a certain read depth of 25K median valid reads per nucleus is achieved.
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