miRDeep protocols

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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



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

Publications for miRDeep

miRDeep in pipelines

PMCID: 5796217
PMID: 29337929
DOI: 10.3390/ijms19010271

[…] for ribosomal rna (rrna), transfer rna (trna), small nucleolar rna (snorna) and repeat sequences, respectively. the remaining reads were used to detect known mirna and predict novel mirna by mirdeep2 software []. the expression profile of srna was normalized in transcripts per million [tpm, tpm = reads (srna)/total reads × 106]. differential expression analysis of mirnas was conducted […]

PMCID: 5838164
PMID: 29507325
DOI: 10.1038/s41598-018-22464-w

[…] candidate sequences were checked using the blastn algorithm from the mirbase (www.mirbase.org) and ncbi databases., for the frequency analysis of all identified mirnas, srna reads were aligned in mirdeep2 software. as reference, we used both previously annotated pre-mirnas from mirbase and the putative pre-mirnas identified in this work. the read counts of identified mirnas in eight libraries […]

PMCID: 5865981
PMID: 29393345
DOI: 10.3892/mmr.2018.8498

[…] [http://hannonlab.cshl.edu/fastx_toolkit/] (). additionally, reads with polya and polyt were also removed, and reads of <15 nucleotides or >34 nucleotides in length were discarded via mirdeep [https://www.mdc-berlin.de/8551903/en/] (). clean sequencing reads from small rna (srna) libraries were summarized for length distribution and srna annotation. the srnas were mapped […]

PMCID: 5887145
PMID: 29467169
DOI: 10.1534/genetics.118.300791

[…] to fastq conversion. all the samples were passed through quality control and sequences with poor base qualities were removed. the adaptor sequences were removed using the clip_adaptors.pl module of mirdeep (v2.0.0.5) (). raw reads were collapsed based on sequence identity using the collapse_reads_md.pl module of mirdeep2. collapsed reads were further annotated for mirna by mapping to mirbase […]

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

[…] 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 […]

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miRDeep in publications

PMCID: 5948824
PMID: 29751742
DOI: 10.1186/s12864-018-4736-4

[…] entries in the rfam database (http://rfam.xfam.org). the remaining sequences were considered as candidate mirnas. with mirbase as a reference (http://www.mirbase.org), we used a modified version of mirdeep2 [] (https://www.mdc-berlin.de/8551903/en/) and srna-tools-cli (http://srna-tools.cmp.uea.ac.uk/) to predict secondary structures. mirevo [] and mirdeep2 [] were then used to predict novel […]

PMCID: 5941544
PMID: 29739311
DOI: 10.1186/s12864-018-4727-5

[…] and wheat genome. the filtered small rna sequences were searched for conserved or known mirna without mismatch. mirbase21.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential mirna and draw the secondary structures. in addition, srna precursors containing classic hairpin structure of mirna but not mapped […]

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

[…] remodelling and transcriptional regulation (fig. ).figure 5, small rna-seq datasets for okf6/tert1-parental, okf6/tert1-tobacco and okf6/tert1-smoke cells were analyzed for novel mirnas using mirdeep2. novel mirna with mirdeep2 score ≥1, ≥8 reads supporting mature mirna, and ≥2 reads supporting loop/star sequence were filtered to acquire high confidence list. this led us to identify 3 […]

PMCID: 5944317
PMID: 29774043
DOI: 10.3389/fpls.2018.00589

[…] bowtie software (v. 1.0.1; langmead et al., ) and up to three mismatches were allowed in alignments., mirna prediction was performed with mirdeep-p (v. 1.3; yang and li, ), a modified version of the mirdeep algorithm (friedländer et al., ) that incorporates an adapted scoring system for plant mirna biogenesis. non-annotated small rna sequences as well as those annotated as mature mirnas […]

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

[…] 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.table 1disease condition […]

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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 ( [email protected]) for any assistance.