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.
Reference Genome Needed:
Installation/User Level: intermediate
Precomputed Target Results Available For Download:
Input Data Required: