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ShortStack


Novel miRNA/Precursor Prediction Sequencing Analysis


ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes. ShortStack discovers small RNA ‘clusters’ de novo, based on user-set thresholds, and annotates clusters with respect to small RNA size, orientation, and repetitiveness. ShortStack also discovers and annotates MIRNA genes. In addition, ShortStack includes a robust method to detect genes producing small RNAs in a phased manner. It outputs a descriptive table of all results, useful genome browser tracks, and detailed text-based alignments of all MIRNAs. It can also be used to quantify a set of input loci with genomic coordinates determined a priori by the user.

Homepage: Link

Reference: [Journal]

Organism Specific:
  • any

    • Reference Genome Needed:
    Online/Local: /
    Installation/User Level: intermediate
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    Algorithm: filter-based
    License: GNU
    Input Data Required:
  • small RNA-seq data
  • genome data

    • Sequencing Analysis
    Algorithm Features:
  • novel miRNA Identification
  • known miRNA identification
  • precursor prediction
  • other ncRNA identification

    • Sequencing Platform Specific: Illumina
    PARE/CLIP-Seq: /
    Novel miRNA/Precursor Prediction
    Prediction Features:
  • sequence
  • structure

    • NGS Data Needed:





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