Linux for Genomics


Date:

Thursday 18 May 2017, 09:00-17:00

Venue:

The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK

Registration deadline:

Thursday 4 May 2017 noon

Cancellation deadline:

Thursday 11 May 2017 noon

Places:

20 (first come, first served)

Registration fee:

£175 (includes coffee/tea and lunch)

Information:

Bert Overduin

Next date(s):

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)


Instructor

Dr. Bert Overduin (Training and Outreach Bioinformatician, Edinburgh Genomics)

Workshop format

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.

Requirements

A general understanding of molecular biology and genomics, and elementary skills in computer usage are required.


Covered topics

The shell and commands
Getting help
Files and directories
Navigating the file system
File management
Permissions
Accessing files
Downloading remote files
Zipping and unzipping files
Pipes and redirects
Filtering / manipulating file content
Shell scripts
Process management
Command-line tools for genomics (seqtk, bioawk, samtools, bedtools, tabix)