Thibodeau, AsaEroglu, AlperMcGinnis, Christopher S.Lawlor, NathanNehar-Belaid, DjamelKursawe, RomyMarches, RaduConrad, Daniel N.Kuchel, George A.Gartner, Zev J.Banchereau, JacquesStitzel, Michael L.Çiçek, A. ErcümentUcar, Duygu2022-02-112022-02-112021-121474-7596http://hdl.handle.net/11693/77279Detecting 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.EnglishMultipletsDoubletsSingle nucleus ATAC-seqsnATAC-seqArticle10.1186/s13059-021-02469-x1474-760X