Bioinformatics Seminars

Bioinformatics Seminar

Time: 10:45am Tuesdays.
Venue:
Level 7 Seminar Room 2, WEHI1

1 May 2018

Actual location : Seminar Room 1

Designing a single cell RNAseq benchmarking dataset to compare protocols and analysis methods

Luyi Tian
WEHI Molecular Medicine

Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis, which has resulted in an explosion of methods development for scRNA-seq. However, the lack of a controlled benchmarking dataset makes it difficult for researchers to evaluate the assumptions behind each method and objectively compare the different methods. To address these problems, we designed a comprehensive benchmark dataset that comprised different levels biological variations and processed through different protocols. We used this dataset to compare different protocols, exam popular assumptions made for scRNA-seq dataset and compare methods for multiple scRNA-seq tasks ranging from normalization to trajectory analysis. We found significant difference in results from different methods and suggested some assumptions for scRNA-seq may be biased. Our dataset and analysis are valuable resource for understanding the nature of scRNA-seq data and help future studies in evaluating their methods.


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