Virus detection using small RNA-seq

This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. The course takes about 5 hours. You will learn how to

  • run VirusDetect and interpret the result files
  • subtract reads originating from the host genome
  • set parameters for filtering the BLAST matches

Course material (2018) is available at the course website and it includes:

  • slides
  • lecture video from a webinar
  • exercises (data is available on Chipster server in the example sessions listed in the exercise sheets, and we also provide ready-made analysis sessions which you can use as a reference when doing exercises on your own)
    1. Potato dataset with different amounts of reads.
    2. Rasberry dataset demonstrates how to provide the host genome.

Scientific topics: RNA-Seq

Resource type: course materials, Video

Difficulty level: Beginner

Authors: Eija Korpelainen

Contributors: Eija Korpelainen

External resources:

Chipster

Virus detection using small RNA-seq https://tess.elixir-europe.org/materials/virus-detection-using-small-rna-seq This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq