XICRA

XICRA analyzes small RNA sequencing data to identify and characterize microRNA isoforms (isomiRs) and to distinguish true biological variations from technical sequencing and processing artifacts.

Key Features:

• IsomiR-Level Analysis: Performs isomiR-level characterization including variants arising from imprecise pre-miRNA processing, non-templated nucleotide additions, and internal base editing.
• Paired-End and Single Reads Comparison: Compares paired-end (PE) and single-read (SR) data to assess whether sequence differences relative to canonical miRNAs are biological or artifacts.
• Detection of Systematic Differences: Identifies systematic differences between SR and PE data, particularly affecting internally edited isomiRs and terminal length-changing isomiRs.
• Reduction of Overestimation Bias: Evaluates the impact of sequencing errors and data processing to reduce overestimation of isomiR abundance and diversity in the isomiRome.
• Read Merging and Comparison: Analyzes single and merged reads from paired-end sequencing to enable comprehensive comparison of isomiR sequences.

Scientific Applications:

• miRNA biology studies: Discriminates true isomiRs from technical noise to study miRNA biogenesis and processing.
• Gene regulation analyses: Enables precise miRNA isoform characterization in genomics and transcriptomics investigations of gene regulation mechanisms.
• Disease pathogenesis research: Improves annotation of isomiRs for studies addressing disease pathogenesis.

Methodology:

Processes small RNAseq data by analyzing single and merged reads from paired-end sequencing and comparing isomiR sequences derived from SR and PE reads to detect systematic differences and minimize false positives.