Journal
BMC BIOINFORMATICS
Volume 15, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/1471-2105-15-144
Keywords
CAGE; Pipeline; Next generation sequencing
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Funding
- Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- RIKEN Omics Science Center from MEXT
- grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan
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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.
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