All the tools you need to analyse your miRNAs


Sequencing Analysis Differential Expression Analysis Known miRNA Identification

Chimira is a web-based system for miRNA analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3′-modifications, 5′-modifications and also internal modifications or variation.

Homepage: Link

Last Software Update: Jan. 22, 2016
Publication Date: June 20, 2015
Citations: 62 [via Pubmed]

Organism Specific:
  • any (from miRBase)

  • Reference Genome Needed:
    Online/Local: /
    Installation/User Level:
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    Sequencing Analysis
    Algorithm Features:
  • known miRNA identification
  • differential expression

  • Sequencing Platform Specific: Illumina
    PARE/CLIP-Seq: /
    Differential Expression Analysis
    Algorithm: DESeq2
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Known miRNA Identification
    NGS Data Needed:

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