Comprehensive Workflow for Cancer Bioinformatics (from Raw Reads to Clinical Diagnosis)

training
analysis-cancer

#1

Dear All,

I am new to Galaxy. I want to use Galaxy to teach students in 90 mins how to analyze cancer NGS data in an easy way without the need to install command line tools or use R (which I am familiar with).

Is there any way to use Galaxy for that purpose? Any recommended tutorials or workflow that can help?

I appreciate your response.

Best Wishes,

Mohamed


#2

Have a look at https://training.galaxyproject.org/


#3

As @marten mentioned already, https://training.galaxyproject.org is the way to go and if you need training resources for an entire classroom you could apply for https://galaxyproject.eu/tiaas.


#4

There is, currently, no perfect training material tailor-made for cancer data analysis. If what you have in mind, when you say cancer NGS data, is exome sequencing data to call somatic variants from, then I’m currently working on such a tutorial, and it should be finished and get included at https://training.galaxyproject.org/ within the next 2 weeks or so. Until then, https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html may be the closest to what you’re actually looking for.


#5

Update: The somatic variants tutorial I mentioned before is available now at https://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/somatic-variants/tutorial.html.

Working through it will take substantially longer than the 90 mins you gave as your requirement, but if you run all the steps before the actual variant calling prior to your exercises with your students, and have them start from BAM datasets of mapped and postprocessed sequencing reads, you may be able to just squeeze it into your time frame.