isoMiRmap

isoMiRmap identifies and exhaustively reports isomiRs from short RNA-seq datasets to enable analysis of miRNA isoform variation at 5' and 3' termini, 3' non-templated additions, and sequence variants such as single-nucleotide polymorphisms (SNPs) and somatic mutations.

Key Features:

• Fast Processing: Capable of analyzing short RNA-seq datasets (e.g., 50 million reads) in just a few minutes on an average laptop.
• Deterministic and Exhaustive Reporting: Deterministically reports all isomiRs present without double-counting to ensure comprehensive coverage.
• Precursor Mapping and Ambiguity Tagging: Provides miRNA precursor locations and tags ambiguous isomiRs whose sequences overlap with known miRNA sequences.
• Variant Detection: Identifies common single-nucleotide polymorphisms (SNPs) and somatic mutations within isomiR sequences.
• Non-Templated Addition Detection: Detects isomiRs with 3' non-templated post-transcriptional additions.
• Output Formats: Produces outputs in HTML, miRGFF3, and tab-delimited formats for downstream integration.

Scientific Applications:

• Genetic Ancestry Studies: Profiling isomiR diversity across populations to investigate ancestry-associated miRNA variation.
• Tissue-Specific Expression: Characterizing tissue-specific miRNA isoform repertoires and 5'/3' end variation.
• Disease Subtype and Cancer Genomics: Comparing isomiR profiles across disease subtypes and cancer samples to explore disease-associated isoform changes.
• miRNA Regulation and Function: Enabling studies of post-transcriptional modifications and sequence variants that affect miRNA regulation and function.

Methodology:

Directly processes short RNA-seq datasets to identify and quantify all isomiRs using a deterministic algorithm that distinguishes bona fide isomiRs from ambiguous ones and reports transcriptional origin information.