Avadis NGS supports an extensive workflow for the analysis of small RNA data. It provides the ability to determine the expression levels of various small RNA species. It supports detection of novel small RNA genes, and prediction of their type. It provides the ability to identify differentially expressed small RNA genes, and visualize the results in a small RNA-specific gene view. The mRNA targets of interesting small RNA genes can be identified from multiple target prediction databases.
Comprehensive Small RNA annotations and structures including miRNA, tRNA, snRNA, and snoRNA from multiple sources.
Support for alignment using the in-built COBWeb alignment algorithm, with support for adapter trimming including adapter mismatches.
Annotation based quality control visualizations in addition to read level quality plots and filters.
Find the expression levels of small RNA genes and mature miRNAs. Normalize the read counts using the approach of DESeq, TMM, or Quantile normalization. Visualize results in the small RNA Gene View.
Novel Small RNA discovery
Detect novel small RNA genes and classify them as miRNA, snoRNA, scRNA, or tRNA. Identify high-confidence predictions with confidence values and conservation scores. Find annotation discrepancies of known genes from the read coverage patterns.
t-Test, Mann-Whitney, n-way ANOVA, and MTC for identifying differentially expressed small RNA genes under different experimental conditions.
miRNA Target Analysis
Use the packaged database of 2 million interactions (with supporting PubMed references) to find relationships between target mRNA genes.