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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.
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Friday, June 30 • 16:41 - 16:47
Galaxy at scale: Analyzing thousands of single cell transcriptomes

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Authors
Mo Heydarian 1, Enis Afgan 1, James Taylor 1*

1 : Johns Hopkins University
* : Corresponding author

Abstract
Single cell sequencing assays are quickly being adopted in biological research. The rapid rate of standardization and optimization of such assays as single-cell RNA-sequencing (scRNA-seq) requires computational pipelines to cope with these large, complex datasets. Here we present the re-analysis of a scRNA-seq study (GSE81682) on thousands of hematopoietic cells using Galaxy. With only minor modifications to Galaxy using Cloudman and Amazon Web Services, we were able to quantify expression of over 100,000 transcripts across 3,840 individual cells. Using collections to operate on thousands of datasets allowed us to generate a standardized workflow to monitor and filter cells based on quality metrics, generate quality reports on subpopulations of cells, and produce expression tables ready for downstream analysis. This analysis demonstrates Galaxy's ability to scale and reproducibly handle complex pipelines totaling over 100,000 intermediate datasets.

Instructors
avatar for Mo Heydarian

Mo Heydarian

Galaxy Project, Johns Hopkins University


Friday June 30, 2017 16:41 - 16:47
Einstein Auditorium Le Corum, Level 0

Attendees (8)