MOIRAI: a compact workflow system for CAGE analysis

Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5' ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level...

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Bibliographic Details
Published in:BMC bioinformatics 2014-05, Vol.15 (1), p.144-144, Article 144
Main Authors: Hasegawa, Akira, Daub, Carsten, Carninci, Piero, Hayashizaki, Yoshihide, Lassmann, Timo
Format: Article
Language:English
Subjects:
Automation
Data processing
Gene expression
Gene Expression Profiling - methods
Genes
Genomes
High-Throughput Nucleotide Sequencing - methods
Humans
Information management
Innovations
K562 Cells
Life sciences
Medicin och hälsovetenskap
Methods
Molecular Sequence Annotation
Operating systems
Programming languages
Quality control
Software
Studies
Technology application
Workflow
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Description
Summary:Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5' ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project but presently there is no software package to perform the essential data processing steps. Here we describe MOIRAI, a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. We will describe three main workflows allowing users to map, annotate and perform an expression analysis over multiple samples. Due to the many built in quality control features MOIRAI is especially suitable to support the development of new sequencing based protocols. The MOIRAI source code is freely available at http://sourceforge.net/projects/moirai/.
ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-15-144