The course aims to provide the core skills to manage “big data” in the genomics era.
The course will focus on R programming, basic scripting and data processing.
At the end of the course, the student will know the basics on how to use the main command-line tools for files and strings handling within the context of genomics such as DNA sequence files and pedigree files containing information on individual genotypes.
Specifically we aim to furnish the knowledge to:
- work into a Linux environment and bash scripting
- use R and its libraries for bioinformatic analyses (Bioconductor project)
- collect and collate genetic data from diverse sources
- arranging directories, renaming and archiving files
- convert files from one format into another
- prepare pipelines of commands for repetitive tasks (for instance, same analyses over more samples)
- learn the fundamentals of Perl and Python programming (hacking pre-existing programs to accomplish novel tasks)
The topics will be illustrated using real-life bioinformatic case studies (for instance, GWAS, exome or transcriptome analyses)
|Arnold Robbins, Nelson H. F. Beebe||Classic Shell Scripting: Hidden Commands that Unlock the Power of Unix||O'Reilly Media||2005||0596005954|
The task of the exam consists in verifying the comprehension of course contents and the ability to properly describe their arguments with appropriate scientific language.
Examination methods are the same for students who attended and for those who did not attend the course.
The exam consists of an oral test based on all the course contents
The exam is passed if the evaluation is greater or equal to 18/30.
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