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Marshaling Public Data for Lean and Powerful Splicing Studies


Thursday, January 16, 2020

11:00 AM - 12:00 PM


Bethesda, 37 4041/4107


Amy Stonelake 240-760-6314


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Event Description

The Sequence Read Archive (SRA) now contains over a million accessions. Such archives are potential gold mines for researchers, but they are not organized for everyday use by scientists. I will describe our work on making large public RNA sequencing datasets easy to use. I will describe our multi-layered design, with one layer for scalable and uniform analysis (Rail-RNA), another for forming easy-to-use summarized (recount2), and a third for indexing the summaries and making them query-able (Snaptron). I will describe collaborations where these tools were applied to (a) evaluate hypotheses about prevalence or specificity of splicing patterns, (b) characterize completeness of the gene annotations we use to understand splicing patterns, and (c) reveal patterns in public data that ultimately changed the study design and allowed more targeted hypotheses to be tested with less new data generation.

Featured Speaker(s)

Dr. Ben Langmead Johns Hopkins University

Sponsored By

Cancer for Center Research