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

Abstract 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...

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Main Authors:	Asa Thibodeau, Alper Eroglu, Christopher S. McGinnis, Nathan Lawlor, Djamel Nehar-Belaid, Romy Kursawe, Radu Marches, Daniel N. Conrad, George A. Kuchel, Zev J. Gartner, Jacques Banchereau, Michael L. Stitzel, A. Ercument Cicek, Duygu Ucar
Format:	Article
Language:	English
Published:	BMC 2021-09-01
Series:	Genome Biology
Subjects:	Multiplets Doublets Single nucleus ATAC-seq snATAC-seq
Online Access:	https://doi.org/10.1186/s13059-021-02469-x

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spelling	doaj-16ab6a3786b04036bf43b168af9640022021-09-05T11:49:14ZengBMCGenome Biology1474-760X2021-09-0122111910.1186/s13059-021-02469-xAMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq dataAsa Thibodeau0Alper Eroglu1Christopher S. McGinnis2Nathan Lawlor3Djamel Nehar-Belaid4Romy Kursawe5Radu Marches6Daniel N. Conrad7George A. Kuchel8Zev J. Gartner9Jacques Banchereau10Michael L. Stitzel11A. Ercument Cicek12Duygu Ucar13The Jackson Laboratory for Genomic MedicineThe Jackson Laboratory for Genomic MedicineDepartment of Pharmaceutical Chemistry, University of CaliforniaThe Jackson Laboratory for Genomic MedicineThe Jackson Laboratory for Genomic MedicineThe Jackson Laboratory for Genomic MedicineThe Jackson Laboratory for Genomic MedicineDepartment of Pharmaceutical Chemistry, University of CaliforniaUniversity of Connecticut Center on Aging, UConn Health CenterDepartment of Pharmaceutical Chemistry, University of CaliforniaThe Jackson Laboratory for Genomic MedicineThe Jackson Laboratory for Genomic MedicineComputer Engineering Department, Bilkent UniversityThe Jackson Laboratory for Genomic MedicineAbstract 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.https://doi.org/10.1186/s13059-021-02469-xMultipletsDoubletsSingle nucleus ATAC-seqsnATAC-seq
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Asa Thibodeau Alper Eroglu Christopher S. McGinnis Nathan Lawlor Djamel Nehar-Belaid Romy Kursawe Radu Marches Daniel N. Conrad George A. Kuchel Zev J. Gartner Jacques Banchereau Michael L. Stitzel A. Ercument Cicek Duygu Ucar
spellingShingle	Asa Thibodeau Alper Eroglu Christopher S. McGinnis Nathan Lawlor Djamel Nehar-Belaid Romy Kursawe Radu Marches Daniel N. Conrad George A. Kuchel Zev J. Gartner Jacques Banchereau Michael L. Stitzel A. Ercument Cicek Duygu Ucar AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data Genome Biology Multiplets Doublets Single nucleus ATAC-seq snATAC-seq
author_facet	Asa Thibodeau Alper Eroglu Christopher S. McGinnis Nathan Lawlor Djamel Nehar-Belaid Romy Kursawe Radu Marches Daniel N. Conrad George A. Kuchel Zev J. Gartner Jacques Banchereau Michael L. Stitzel A. Ercument Cicek Duygu Ucar
author_sort	Asa Thibodeau
title	AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data
title_short	AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data
title_full	AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data
title_fullStr	AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data
title_full_unstemmed	AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data
title_sort	amulet: a novel read count-based method for effective multiplet detection from single nucleus atac-seq data
publisher	BMC
series	Genome Biology
issn	1474-760X
publishDate	2021-09-01
description	Abstract 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.
topic	Multiplets Doublets Single nucleus ATAC-seq snATAC-seq
url	https://doi.org/10.1186/s13059-021-02469-x
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AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data

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