miRDeep specifications

Information


Unique identifier OMICS_00373
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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Maintainers


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

miRDeep articles

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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Desktop
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.

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