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miRDeep specifications


Unique identifier OMICS_00373
Name miRDeep
Alternative name miRDeep2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes




No version available


  • person_outline Nikolaus Rajewsky
  • person_outline Jiyuan An
  • person_outline Colleen Nelson

Publications for miRDeep

miRDeep citations


Cigarette smoke and chewing tobacco alter expression of different sets of miRNAs in oral keratinocytes

Sci Rep
PMCID: 5935709
PMID: 29728663
DOI: 10.1038/s41598-018-25498-2

[…] entification. These reads were first aligned to mature and precursor sequence from miRBase 21 miRNA database (Human) using Bowtie. Unaligned reads were further aligned against human genome hg19 using miRDeep2 (version Known miRNA that are quantified with at least 10 reads in both samples of a pairs i.e. OKF6/TERT1-Tobacco vs. OKF6/TERT1-Parental and OKF6/TERT1-Smoke vs. OKF6/TERT1-Parent […]


Robust Sub nanomolar Library Preparation for High Throughput Next Generation Sequencing

BMC Genomics
PMCID: 5935984
PMID: 29728062
DOI: 10.1186/s12864-018-4677-y

[…] First, Cutadapt 1.9.1 was used to trim Illumina TruSeq adapter sequences from fastq files at 3′ ends. Subsequently, for microRNA, miRDeep2 v. was used to map the reads to the miRBase (version 21) microRNA database and quantify microRNA expression levels. For other small noncoding RNA, data were analyzed using Qiagen (Germ […]


An integrated view of the role of miR 130b/301b miRNA cluster in prostate cancer

PMCID: 5930504
PMID: 29744254
DOI: 10.1186/s40164-018-0102-0

[…] inition. Data not available in repositories was extracted from the original article. Martens-Uzunova et al. RNA-seq data [] was provided by the authors; it was normalized, counted and annotated using miRDeep2 software using default parameters [] and miRBase database Release 21. The small RNA-seq data from the TCGA-PRAD was retrieved as explained in the next section. […]


Differentially expressed microRNAs associated with changes of transcript levels in detoxification pathways and DDT resistance in the Drosophila melanogaster strain 91 R

PLoS One
PMCID: 5919617
PMID: 29698530
DOI: 10.1371/journal.pone.0196518

[…] a) were accepted and retained for the further analysis. The sRNA sequencing data with annotated tags were deposited to NCBI Short Read Archive (SRA) with the accession number SRP136631. Additionally, miRDeep2 v.0.0.8 software was used in order to predict novel miRNA candidates []. Illumina adapters of sRNA raw sequence reads were trimmed using cutadapt v.1.15 []. The trimmed reads were quality-che […]


IFN λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs

PLoS One
PMCID: 5909910
PMID: 29677213
DOI: 10.1371/journal.pone.0194765
call_split See protocol

[…] mmarized in . Adaptor sequences from the library preparation and sequencing were trimmed from the reads using Cutadapt v. 1.8 [], retaining only reads with a minimum length of 16 nt. Modules from the miRDeep2 package v. was applied for the remaining sequencing data processing [], using the mapper module to collapse trimmed reads and Bowtie v. 1.0.0 [] for the mapping of reads to a pre-buil […]


Comparative transcriptome analysis to investigate the potential role of miRNAs in milk protein/fat quality

Sci Rep
PMCID: 5908868
PMID: 29674689
DOI: 10.1038/s41598-018-24727-y

[…] only expressed miRNAs. miRNAs whose expression was significantly lower or higher in one group than in any other group (FDR ≤ 0.05, |log2 (fold change)| ≥ 1) were referred to as DE miRNAs. We used the miRDeep2 package (Ver., which discovers miRNA genes by analyzing sequenced RNAs, to predict novel and known miRNAs. This tool reports known and novel microRNAs with high accuracy in seven spec […]


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miRDeep institution(s)
Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology at the Max-Delbruck-Center for Molecular Medicine, Berlin-Buch, Germany; Laboratory for New Sequencing Technology, Berlin Institute for Medical Systems Biology at the Max-Delbruck-Center for Molecular Medicine, Berlin-Buch, Germany
miRDeep funding source(s)
Supported by the Helmholtz-Alliance on Systems Biology (Max Delbruck Centrum Systems Biology Network); the Helmholtz Association; the German Ministry of Education and Research (BMBF), the Senate of Berlin by funds for the Berlin Institute for Medical Systems Biology (BIMSB) (315362A); and China Scholarship Council.

miRDeep review

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Raja Ishaq

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Wonderful tool to find microRNA fro Transcriptome data along with their relative abundance. It works well not only on Mac and Linux but also on Windows. Yes, it demands basic command line expertise but its prediction based results are trustworthy. Free to use. All it takes, is a just quality checked the file of reads in fasta, fastq, seq.txt or qseq.txt format and indexed reference genome.In mirdeep2, Initially, the reads are subject to mapper.pl through use of a command line that has the provision of changing the format of the input file to required fasta format , clipping a particular adapter sequence , removing non-canonical letters , removing reads below a particular threshold and then mapping the output reads with indexed reference genome . Two output files are obtained by running mapper.pl, one fasta file of clean trimmed reads and other arf file of mapped reads.The fasta file of trimmed reads is then subjected to quantifier.pl, where in there is a provision of mapping the reads with predefined precursor sequences and predefined mature miRNA sequence of reference individual to determine the expression of corresponding miRNA present in the input file.The purposeful output file comes in csv form that contains all the miRNA identifiers along with their read count and can be used to find DEG. For the benefit of newcomers, I suggest BOWTIE to index reference genome and mirbase.org to get predefined Precursor miRNA and mature miRNA of reference species . Feel free to communicate by mail ( ishaaq.raja@gmail.com) for any assistance.