Linux for Genomics
Thursday 18 May 2017, 09:00-17:00
The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK
Thursday 4 May 2017 noon
Thursday 11 May 2017 noon
20 (first come, first served)
£175 (includes coffee/tea and lunch)
31 August 2017
Genomic studies produce vast amounts of data, usually in the form of very large text files. Linux is particularly suited to working with such files, and is therefore arguably one of the most important tools in a bioinformatician’s toolkit. The Linux command-line enables one to view, filter and manipulate large text files that are difficult or impossible to handle with applications like Word or Excel, write pipelines to perform certain tasks, and run bioinformatics software for which no web interface is available. In this workshop we will first cover the most used Linux commands, followed by a short introduction to several popular command-line tools that were especially developed for genomics as well as file formats commonly used in genomics (BED, FASTA, FASTQ, GFF/GTF, SAM/BAM, VCF).
"Having never used Linux before I came away with a working knowledge of the command-line and the confidence to use it." (May 2016)
Dr. Bert Overduin (Training and Outreach Bioinformatician, Edinburgh Genomics)
The workshop consists of guided tutorials and hands-on exercises. Roughly 3/4 of the workshop will be spent on Linux and 1/4 on command-line tools for genomics and file formats.
Who should attend
Graduates, postgraduates, and PIs, without any previous command-line experience, who want to learn to use the Linux command-line in order to be able to work with large data files.
A general understanding of molecular biology and genomics, and elementary skills in computer usage are required.
The shell and commands
Files and directories
Navigating the file system
Downloading remote files
Zipping and unzipping files
Pipes and redirects
Filtering / manipulating file content
Command-line tools for genomics (seqtk, bioawk, samtools, bedtools, tabix)