What can the UEA sRNA Workbench do for you?

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 generate secondary structure plots of RNA sequences please use the RNA Annotation tool. A tutorial on how to use the RNA Annotation tool can be found here.

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

  • silvia

    Hello,
    I have smallRNA-seq (fastq files) in 2 different conditions, 3 replicates for each and I’d like to know which miRNAs are differentially expressed. Can UEA small RNA Workbench help me? If yes, do you mind to give me some tips to perform the analysis?
    Thank you.
    Silvia

    • The sRNA Workbench

      Hi Silvia,

      Sorry for the delay in response I was on leave,

      Yes, this tool can hopefully help. To begin with you must first trim the adapters and convert the FASTQ data to FASTA. You can use the adapter removal tool (select show version 3.2 from the menu and then find the adapter removal tool from the drop downs) a tutorial on the adapter removal tool can be found on the website under the tutorials drop down menu.

      When you have your trimmed sequences use the QC->normalisation-> DE pipeline. A tutorial on using this pipeline can also be found in the tutorials section.

      Hope this helps, please let me know if you need further assistance!

      Cheers,
      Matt

A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices