However, there is a need for new methods that can summarize alternative splicing across thousands of public data sets in a unified manner, without relying on prior transcript annotation 28, 29. Numerous algorithms for alternative splicing analysis have been developed 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, including several recent studies that propose useful models for studying complex splicing patterns in RNA-Seq data 11, 13, 25. RNA-Seq has accelerated our understanding of how alternative splicing networks are coordinated, in part through the meta-analysis of RNA-Seq data gathered from many independent experiments 9, 10. RNA splicing is governed by both cis-regulatory elements (specific sequences in the pre-mRNA that influence the strength of a splice site) and trans-acting splicing factors (RNA-binding proteins that can act as either splicing enhancers or repressors). In this work we focus on the alternative splicing use case for RNA-Seq data.Īlternative splicing of pre-mRNA (RNA splicing) is a highly regulated process that generates extensive transcriptomic and proteomic diversity across all cell types. Together, these allow researchers to query publicly available RNA-Seq data in a standardized and reproducible manner. 7) resource and accompanying Snaptron 8 query engine. To address this, we previously developed a bioinformatics pipeline (Rail-RNA) 5, 6 and created the recount2 (ref. Likewise, the need to analyze this data from scratch leads to unnecessary duplications of effort across research groups 3, 4.
Drawing new conclusions from many raw RNA-Seq data sets requires a level of computational power and expertise that is out of reach for most labs. However, public archives store raw, unprocessed data.
#MESASQLITE ALTERNATUVE ARCHIVE#
Its utility has made it one of the most common experimental data types stored in the Sequence Read Archive 1 and other related international archives 2.
RNA-Seq is a powerful tool for studying gene expression, alternative splicing, and post-transcriptional regulation.
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