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MOIRAI: a compact workflow system for CAGE analysis

BACKGROUND: 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 expressio...

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Autores principales: Hasegawa, Akira, Daub, Carsten, Carninci, Piero, Hayashizaki, Yoshihide, Lassmann, Timo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033680/
https://www.ncbi.nlm.nih.gov/pubmed/24884663
http://dx.doi.org/10.1186/1471-2105-15-144
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author Hasegawa, Akira
Daub, Carsten
Carninci, Piero
Hayashizaki, Yoshihide
Lassmann, Timo
author_facet Hasegawa, Akira
Daub, Carsten
Carninci, Piero
Hayashizaki, Yoshihide
Lassmann, Timo
author_sort Hasegawa, Akira
collection PubMed
description BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: Due to the many built in quality control features MOIRAI is especially suitable to support the development of new sequencing based protocols. AVAILIABILITY: The MOIRAI source code is freely available at http://sourceforge.net/projects/moirai/.
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spelling pubmed-40336802014-05-27 MOIRAI: a compact workflow system for CAGE analysis Hasegawa, Akira Daub, Carsten Carninci, Piero Hayashizaki, Yoshihide Lassmann, Timo BMC Bioinformatics Software BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: Due to the many built in quality control features MOIRAI is especially suitable to support the development of new sequencing based protocols. AVAILIABILITY: The MOIRAI source code is freely available at http://sourceforge.net/projects/moirai/. BioMed Central 2014-05-16 /pmc/articles/PMC4033680/ /pubmed/24884663 http://dx.doi.org/10.1186/1471-2105-15-144 Text en Copyright © 2014 Hasegawa et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Hasegawa, Akira
Daub, Carsten
Carninci, Piero
Hayashizaki, Yoshihide
Lassmann, Timo
MOIRAI: a compact workflow system for CAGE analysis
title MOIRAI: a compact workflow system for CAGE analysis
title_full MOIRAI: a compact workflow system for CAGE analysis
title_fullStr MOIRAI: a compact workflow system for CAGE analysis
title_full_unstemmed MOIRAI: a compact workflow system for CAGE analysis
title_short MOIRAI: a compact workflow system for CAGE analysis
title_sort moirai: a compact workflow system for cage analysis
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033680/
https://www.ncbi.nlm.nih.gov/pubmed/24884663
http://dx.doi.org/10.1186/1471-2105-15-144
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