AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data

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buir.contributor.authorÇiçek, A. Ercüment
buir.contributor.orcidÇiçek, A. Ercüment|0000-0001-8613-6619
dc.citation.epage19en_US
dc.citation.issueNumber1en_US
dc.citation.spage1en_US
dc.citation.volumeNumber22en_US
dc.contributor.authorThibodeau, Asa
dc.contributor.authorEroglu, Alper
dc.contributor.authorMcGinnis, Christopher S.
dc.contributor.authorLawlor, Nathan
dc.contributor.authorNehar-Belaid, Djamel
dc.contributor.authorKursawe, Romy
dc.contributor.authorMarches, Radu
dc.contributor.authorConrad, Daniel N.
dc.contributor.authorKuchel, George A.
dc.contributor.authorGartner, Zev J.
dc.contributor.authorBanchereau, Jacques
dc.contributor.authorStitzel, Michael L.
dc.contributor.authorÇiçek, A. Ercüment
dc.contributor.authorUcar, Duygu
dc.date.accessioned2022-02-11T10:49:17Z
dc.date.available2022-02-11T10:49:17Z
dc.date.issued2021-12
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractDetecting 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.en_US
dc.identifier.doi10.1186/s13059-021-02469-xen_US
dc.identifier.eissn1474-760X
dc.identifier.issn1474-7596
dc.identifier.urihttp://hdl.handle.net/11693/77279
dc.language.isoEnglishen_US
dc.publisherBioMed Central Ltd.en_US
dc.relation.isversionofhttps://doi.org/10.1186/s13059-021-02469-xen_US
dc.source.titleGenome Biologyen_US
dc.subjectMultipletsen_US
dc.subjectDoubletsen_US
dc.subjectSingle nucleus ATAC-seqen_US
dc.subjectsnATAC-seqen_US
dc.titleAMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq dataen_US
dc.typeArticleen_US
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