SePIA : RNA and small RNA sequence processing, integration, and analysis

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Icay , K , Chen , P , Cervera Taboada , A , Rantanen , V , Lehtonen , R & Hautaniemi , S 2016 , ' SePIA : RNA and small RNA sequence processing, integration, and analysis ' , BioData mining , vol. 9 , 20 . https://doi.org/10.1186/s13040-016-0099-z

Title: SePIA : RNA and small RNA sequence processing, integration, and analysis
Author: Icay, Katherine; Chen, Ping; Cervera Taboada, Alejandra; Rantanen, Ville; Lehtonen, Rainer; Hautaniemi, Sampsa
Contributor: University of Helsinki, Research Programs Unit
University of Helsinki, Research Programs Unit
University of Helsinki, Research Programs Unit
University of Helsinki, Research Programs Unit
University of Helsinki, Research Programs Unit
University of Helsinki, Medicum
Date: 2016-05-20
Language: eng
Number of pages: 18
Belongs to series: BioData mining
ISSN: 1756-0381
URI: http://hdl.handle.net/10138/164695
Abstract: Background: Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed. Such studies would benefit from a computational workflow that is easy to implement and standardizes the processing and analysis of both sequenced data types. Results: We developed SePIA (Sequence Processing, Integration, and Analysis), a comprehensive small RNA and RNA workflow. It provides ready execution for over 20 commonly known RNA-seq tools on top of an established workflow engine and provides dynamic pipeline architecture to manage, individually analyze, and integrate both small RNA and RNA data. Implementation with Docker makes SePIA portable and easy to run. We demonstrate the workflow's extensive utility with two case studies involving three breast cancer datasets. SePIA is straightforward to configure and organizes results into a perusable HTML report. Furthermore, the underlying pipeline engine supports computational resource management for optimal performance. Conclusion: SePIA is an open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA's modular design enables robust customization to a given experiment while maintaining overall workflow structure.
Subject: Sequencing
Integration
miRNA
totalRNA
RNA
Breast cancer
BREAST-CANCER
SEQ DATA
DIFFERENTIAL EXPRESSION
SIGNALING PATHWAY
GENE-EXPRESSION
QUALITY-CONTROL
READ ALIGNMENT
MIRNA
QUANTIFICATION
MODULATION
3111 Biomedicine
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