CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data

BMC Genomics

Jean-Pierre Kocher¹  Huihuang Yan¹  Matthew Bockol¹  Sumit Middha¹  Aditya Bhagwate¹  Jared Evans¹  Zhifu Sun¹ 

[1] Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA

关键词: Variant detection;    Differential expression;    Analysis pipeline;    miRNA sequencing;   

Others  :  1216728
DOI  :  10.1186/1471-2164-15-423

 received in 2014-03-09, accepted in 2014-05-27,  发布年份 2014

【 摘 要 】

Background

miRNAs play a key role in normal physiology and various diseases. miRNA profiling through next generation sequencing (miRNA-seq) has become the main platform for biological research and biomarker discovery. However, analyzing miRNA sequencing data is challenging as it needs significant amount of computational resources and bioinformatics expertise. Several web based analytical tools have been developed but they are limited to processing one or a pair of samples at time and are not suitable for a large scale study. Lack of flexibility and reliability of these web applications are also common issues.

Results

We developed a Comprehensive Analysis Pipeline for microRNA Sequencing data (CAP-miRSeq) that integrates read pre-processing, alignment, mature/precursor/novel miRNA detection and quantification, data visualization, variant detection in miRNA coding region, and more flexible differential expression analysis between experimental conditions. According to computational infrastructure, users can install the package locally or deploy it in Amazon Cloud to run samples sequentially or in parallel for a large number of samples for speedy analyses. In either case, summary and expression reports for all samples are generated for easier quality assessment and downstream analyses. Using well characterized data, we demonstrated the pipeline’s superior performances, flexibility, and practical use in research and biomarker discovery.

Conclusions

CAP-miRSeq is a powerful and flexible tool for users to process and analyze miRNA-seq data scalable from a few to hundreds of samples. The results are presented in the convenient way for investigators or analysts to conduct further investigation and discovery.

【 授权许可】

   
2014 Sun et al.; licensee BioMed Central Ltd.

【 图 表 】

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