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Novel smallRNA

Parent category smallRNA
Description Components that identify and analyze putative novel miRNAs and other smallRNAs.
Component Version Inputs Outputs Description
NCRNAAnnot 1.0 expression, gtf annotated Creates reference files for gene features and known ncRNAs and creates additional columns for a putatively novel miRNA expression matrix with information on relative genomic location (e.g. intragenic/intergenic, host gene and transcript) and neighbouring or overlapping ncRNAs.
NovelExprMatrix 1.0 novelArray csv, csv_wID Take output of miRanalyzer (or miRDeep2) and create an expression matrix with the putative novel miRNAs found.
NovelMatureSeq 0.1 novel, fqFiles mature, array Given a set of putative novel miRNA regions (e.g. output from miRanalyzer or miRDeep2), retrieves consensus functional "mature" region that can then be used for predicting target genes (e.g. as input to MirMatch.
NovelMirnas 1.0 fqFiles, mirDP_genome, mirDP_mature, mirDP_related_mature, mirDP_precursor array Performs novel miRNA discovery using miRanalyzer or mirDeep2, depending on what is installed and what you want to use.

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