Introduction
sRNAnalyzer is a flexible, modular pipeline for the analysis of small RNA sequencing data. Features include,
- Additional adapter trimming process to generate cleaner data
- Comprehensive microRNA profiling strategies to better handle isomiR issues
- Summarization for each nucleotide to detect potential SNPs on miRNAs
- Multiple assignment to simulate miRNA array and qRT-PCR platforms
- A local probabilistic model to map reads to the most-likely entry IDs
- Comprehensive ribosomal RNA filtering to get more accurate mapping results
- More specific species assignment on exogenous RNAs in circulation
- Taxonomy annotation/summarization at major ranks for exogenous species
Downloads
Download the sRNAnalyzer pipeline and alignment databases as .tar.gz files.
| sRNAnalyzer Pipeline | sRNAnalyzer |
| small RNA Databases | sRNA_DBs |
| Human and Exogenous Databases | MainDBs |
| NCBI Non-Human Databases | NCBI_NonHuman |
| E.Coli Samples for Pipeline Evaluation | E_coli_evaluation_samples |
Web Application
To demonstrate how to use sRNAnalyzer, we built a web interface in a local server, which can be accessed at Web Application page for uploading data and running sRNAnalyzer pipeline online. For testing purpose, Username – ‘isb’ and Password – ‘password’ can be used. For academic use, free accounts will be provided based on email applications. Please send emails to Dr. Kai Wang.
Getting Started
To get started using sRNAnalyzer, download the sRNAnalyzer as a .zip or a .tar.gz file as well as the sRNA databases required. Then head to the Getting Started page for instruction on setting up and running sRNAnalyzer.
Documentation
For more information on options and configuration, head to the Documentation. For documentation on the format of the output and summary files, go to the Output file documentation.