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MOIRAI specifications


Unique identifier OMICS_07115
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, Java, Perl, PHP, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
R, sqlite
Maintained Yes


No version available

Publication for MOIRAI

MOIRAI citations


Restricted Presence of POU6F2 in Human Corneal Endothelial Cells Uncovered by Extension of the Promoter level Expression Atlas

PMCID: 5704063
PMID: 29113774
DOI: 10.1016/j.ebiom.2017.10.024

[…] ed by Helicos. In addition, reads shorter than 20 nucleotides and longer than 70 nucleotides were removed. These filtered reads were mapped to the human genome sequence (hg19), using Delve () and the MOIRAI pipeline platform (). Mapped reads (tags) were counted with respect to the robust peaks identified in the FANTOM5, which was used as a reference for promoter regions (). On the basis of the tot […]


Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

Sci Data
PMCID: 5663209
PMID: 29087374
DOI: 10.1038/sdata.2017.163

[…] o two mismatches) by rRNAdust. The remaining reads were aligned to rheMac8 reference genome using the probabilistic mapping tool delve (see Code Availability).Data mapping workflow was implemented in Moirai, a system that allows creation and customization of sequencing data processing pipelines.Expression quantification was performed as previously described. In short, 1-base pair TSSs were first o […]


Linking FANTOM5 CAGE peaks to annotations with CAGEscan

Sci Data
PMCID: 5625555
PMID: 28972578
DOI: 10.1038/sdata.2017.147
call_split See protocol

[…] de sequence GCTATA, present in every sample, acted as the spacer that we introduced in ref. to decrease the amount of strand-invasion artefacts. The paired-end sequences were then processed with the MOIRAI workflow system, with a template implementing the workflow OP-WORKFLOW-CAGEscan-FANTOM5-v1.0, described below and in .For each pair, the first (CAGE) and second (CAGEscan) reads in FASTQ format […]


FANTOM5 CAGE profiles of human and mouse samples

Sci Data
PMCID: 5574368
PMID: 28850106
DOI: 10.1038/sdata.2017.112

[…] uniform quality assessment of the profiled RNA extracts. The resulting CAGE libraries were sequenced by HeliScope in RIKEN and also in Helicos Biosciences, and the obtained data were processed by the MOIRAI system. Quality of the resulting CAGE profiles was checked with several statistics as well as manual inspection by using the ZENBU browser. Finally CAGE profiles were shared among the consortiu […]


High resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor

Sci Rep
PMCID: 5460231
PMID: 28588247
DOI: 10.1038/s41598-017-02824-8

[…] l sequences were removed using TagDust, and ribosomal RNA sequences were removed with rRNAdust. The resulting extracted CAGE tags were then mapped to the human genome (hg19) using BWA v0.5.9 with the MOIRAI pipeline platform. Mapped CAGE tags were counted with respect to the FANTOM5-defined CAGE peaks, which corresponded to promoters. When multiple CAGE peaks were associated with a single gene, di […]


Single Nucleotide Resolution Mapping of Hepatitis B Virus Promoters in Infected Human Livers and Hepatocellular Carcinoma

J Virol
PMCID: 5110153
PMID: 27681123
DOI: 10.1128/JVI.01625-16

[…] gs to the human genome (hg19/GRCh37 assembly) or to the murine genome (mm9/NCBI37 assembly) in the case of the murine liver transduced with AAV-HBV, using BWA v0.5.9 () with default parameters on the MOIRAI pipeline (). The unmapped tags extracted from the mapping results were aligned to 16 representative HBV genomes downloaded from HBVdb (). Because the HBV genome is circular, each genome was tan […]


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MOIRAI institution(s)
RIKEN Center for Life Science Technologies (CLST), Riken Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan

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