The small RNA analysis tools in Biomedical Genomics Workbench 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. Illumina, 454 and SOLiD sequencing platforms are supported. For SOLiD, adapter trimming and annotation is done in color space.
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 Biomedical Genomics Workbench is (1). This approach has the advantage that it 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 (e.g. 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 Biomedical 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].
In the following, the tools for working with small RNAs are described in detail.
- Extract and count
- Downloading miRBase
- Annotating and merging small RNA samples
- Working with the small RNA sample
- Exploring novel miRNAs