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Basic NGS data analysis using Galaxy@IGC: 11th September at 16h00 in Theano

After our first introductory session, we will now start with our topic-specific sessions.

In the next session, we will:

  • Learn what is a fastq, the raw data coming from sequencing machines
  • Analyse the quality of a fastq file using the tool FastQC.
  • Learn how to improve the quality of your data using trimmomatic and other tools.
  • Learn how to map reads to a reference genome using bwa.
  • Learn what are SAM/BAM alignment files.
  • Learn how to visualize alignment results using IGV

All of this (except the visualization using IGV) will be done using Galaxy through a tutorial. Note: for the visualizaton step you need to install IGV in your laptop.

These steps are mostly the same for all NGS applications that we will cover in the following Galaxy sessions (metagenomics, genomics, transcriptomics, epigenetics).

For those that didn't come to the first session you may find useful to go through an Introductory Galaxy Tutorial.

Another, non-galaxy based material can also be useful.

 

If you're coming to this session, please register by adding your name below: