Small RNA Analysis

Tools for small RNA Analysis previously available under the Microarray and Small RNA Analysis folder of the Toolbox have been deprecated and will be retired in a future version of the software. Small RNA anaysis is now supported by new tools, available under the RNA-Seq and Small RNA Analysis (Image expressionfolder)| miRNA Analysis (Image mirna_tools_folde_open) folder of the Toolbox. Please see miRNA analysis for information about the new tools.

The older small RNA analysis tools have been moved to Legacy Tools (Image legacy_tools) | Small RNA Analysis (legacy) (Image small_rna_folder) folder of the Toolbox, and each tool's name has "(legacy)" appended to it. If you have concerns about the future retirement of these tools, please contact QIAGEN Bioinformatics Support team at [email protected].

The small RNA analysis tools are designed to facilitate trimming of sequencing reads, counting and annotating of the resulting tags using miRBase or other annotation sources and performing expression analysis of the results. The tools are general and flexible enough to accommodate a variety of data sets and applications within small RNA profiling, including the counting and annotation of both microRNAs and other non-coding RNAs from any organism.

The annotation part is designed to make special use of the information in miRBase but more general references can be used as well.

There are generally two approaches to the analysis of microRNAs or other smallRNAs: (1) count the different types of small RNAs in the data and compare them to databases of microRNAs or other smallRNAs, or (2) map the small RNAs to an annotated reference genome and count the numbers of reads mapped to regions which have smallRNAs annotated. The approach taken by CLC Genomics Workbench is (1). This approach does not require an annotated genome for mapping - you can use the sequences in miRBase or any other sequence list of smallRNAs of interest to annotate the small RNAs. In addition, small RNAs that would not have mapped to the genome (for example when lacking a high-quality reference genome, or if the RNAs have not been transcribed from the host genome) can still be measured and their expression be compared. The methods and tools developed for CLC Genomics Workbench are inspired by the findings and methods described in [Creighton et al., 2009], [Wyman et al., 2009], [Morin et al., 2008] and [Stark et al., 2010].