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chevron_left Read quality control Gene set enrichment analysis Known transcript quantification miRNA target prediction Normalization Differential expression Bioinformatics workflows Adapter trimming Spliced read alignment chevron_right
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miARma-Seq specifications


Unique identifier OMICS_13537
Name miARma-Seq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Output format SAM, BAM, PDF, TSV, XLS
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl, Python, R
Computer skills Advanced
Version 1.5.1
Stability Stable
Maintained No


  • Primates
    • Homo sapiens




No version available

Publication for miARma-Seq

miARma-Seq citations


MicroRNA Contents in Matrix Vesicles Produced by Growth Plate Chondrocytes are Cell Maturation Dependent

Sci Rep
PMCID: 5826934
PMID: 29483516
DOI: 10.1038/s41598-018-21517-4
call_split See protocol

[…] RNA was isolated from MVs or cells using TRizol. Next generation sequencing was performed in an Illumina HiSeq. 2500 (Illumina, San Diego, CA). Data normalization and analysis were conducted with the miARma-Seq tool (see supplemental materials). Briefly, sequence quality was assessed with FASTQC; sequence reads were aligned with Bowtie2 to the NCBI Rattus norvegicus annotation release 105 (Rnor_6. […]


The involvement of serum exosomal miR 500 3p and miR 770 3p in aging: modulation by calorie restriction

PMCID: 5814159
PMID: 29464019
DOI: 10.18632/oncotarget.23651

[…] rm was utilized to generate 50 bp single-end sequencing reads (Illumina, CA, USA). Cutadapter 1.11 was applied for data filtering to remove adapters and low quality sequences. For miRNA analysis, the miARma-Seq pipeline with the miRNA analysis workflow was utilized according to the user manual []. The workflow of miRNA analysis with miARma-Seq consisted with alignment with Bowtie2 [] and entity qu […]


Identification and Analysis of P53 Mediated Competing Endogenous RNA Network in Human Hepatocellular Carcinoma

PMCID: 5666336
PMID: 29104512
DOI: 10.7150/ijbs.21502

[…] 3400, GSM1923402, GSM1923401, GSM1923403 . These data were obtained from HepG2 cells, which were treated with same experimental procedures as RNA-Seq. The number of reads of each miRNA was counted by miARma-Seq (v1.5) . The differential expression analysis was performed with the same standard as RNA-seq procedure via edgeR , . […]


Circles reshaping the RNA world: from waste to treasure

Mol Cancer
PMCID: 5345220
PMID: 28279183
DOI: 10.1186/s12943-017-0630-y

[…] RNAs derived from proximal splice sites []. In order to bring together these well-established tools in a single bundle and achieve reliable predictions, Andrés-León, E. et al. developed a suite named miARma-Seq []. This is a comprehensive pipeline analysis which can identify mRNAs, miRNAs and circRNAs in any sequenced organism and enable differential expression, miRNA-mRNA target prediction or fun […]

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miARma-Seq institution(s)
Bioinformatics Unit, Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain; Unidad de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario de Valme, Instituto de Biomedicina de Sevilla (IBIS), Seville, Spain
miARma-Seq funding source(s)
This work was supported by the European Union grant FP7-REGPOT-2012-2013-1.

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