This page details all the functions the UEA sRNA Workbench can perform at a high level and links to the tools that should be used for each task
Preparation of sRNA data
Taking data straight from a sequencing instrument in FASTQ format typically requires any remaining adapter fragments to be stripped from the data. Do do this, use the Adapter Removal tool. A tutorial on how to use the Adapter Removal tool can be found here.
Occasionally, data that has had its adapters trimmed will require further filtering to remove sequences that are of no interest to the user. For example, stripping out T or R RNA sequences, removing sequences that do not match to the reference genome or removing sequences based on their length or abundance in the file (i.e. how many times the small RNA was sequenced during the experiment). To do this, use the Filter tool. A tutorial on how to use the Filter tool can be found here.
Aligning sRNA Data to a long read file such as a Genome
Certain tools within the workbench require an aligned sequence file (such as VisSR) or you may wish to align sequences for another type of analysis. To do this use the Sequence Alignment tool. A tutorial on how to use the Sequence Alignment tool can be found here.
Analysing small RNA data
The UEA sRNA Workbench can perform various types of analysis on prepared small RNA data taken from Next Generation Sequencing experiments. The tool you use for analysis depends on what information you wish to extract from your data. The following list gives a short detail on each analysis type and a link to the tool you should use for this analysis.
- Predicting novel miRNA sequences – miRCat (tutorial)
- Determine normalised expression levels of miRNA sequences found in miRBase from multiple input samples – miRProf (tutorial)
- Compare sRNA expression levels from multiple input samples – SiLoCo (tutorial)
- Predicting phased ta-siRNAs in plant datasets – ta-si Prediction (tutorial)
- Degradome assisted miRNA target prediction – PAREsnip
Visualising small RNA data and results
The UEA sRNA Workbench has various methods for visualising results directly from the analysis tools (see the tutorials for further information). Users can also use these tools independently to view data from other sources or saved data from previous experiments.
If you wish to browse genome files and their associated GFF records containing gene annotations, please use the VisSR tool. Alternatively this tool can be used for viewing sRNA alignments taken directly from the Sequence Alignment tool. A tutorial on how to use the VisSR tool can be found here