138041 - Genotype-free demultiplexing of pooled single-cell RNA-seq.pdf (2.61 MB)
Genotype-free demultiplexing of pooled single-cell RNA-seq
journal contribution
posted on 2023-05-20, 11:56 authored by Xu, J, Falconer, C, Nguyen, Q, Crawford, J, McKinnon, BD, Mortlock, S, Senabouth, A, Andersen, S, Chiu, HS, Jiang, L, Palpant, NJ, Yang, J, Mueller, MD, Alexander HewittAlexander Hewitt, Pebay, A, Montgomery, GW, Powell, JE, Coin, LJMA variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior to pooling. We introduce scSplit which utilizes genetic differences inferred from scRNA-seq data alone to demultiplex pooled samples. scSplit also enables mapping clusters to original samples. Using simulated, merged, and pooled multi-individual datasets, we show that scSplit prediction is highly concordant with demuxlet predictions and is highly consistent with the known truth in cell-hashing dataset. scSplit is ideally suited to samples without external genotype information and is available at: https://github.com/jon-xu/scSplit.
History
Publication title
Genome BiologyVolume
20Article number
290Number
290Pagination
1-12ISSN
1474-760XDepartment/School
Menzies Institute for Medical ResearchPublisher
BioMed Central Ltd.Place of publication
United KingdomRights statement
© The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.Repository Status
- Open