Description: A hands-on interactive course that will introduce you to how to analyse genomic sequences in the command line environment. Examples will focus on metagenomics data but the course is suitable to anyone starting to analyze high-throughput sequencing data.

This course will be taught by Dr. Adina Howe from Iowa State University. Her group focuses on integrating traditional microbiology approaches with metagenomics and computational biology as investigative tools to understand environmental microbial populations

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book by linking here.

Target audience:

• Beginners who have very little background in using the command line and are enthusiastic to learn more
• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
• Further details regarding eligibility criteria are available here
• Further details regarding the charging policy are available here

Duration: 1

Sessions:

Number of sessions: 1

Format: Presentation and demonstrations

Frequency: A number of times per year

Aims: During this course you will learn about:

• the command line
• the shell language
• downloading data from an API
• running a bioinformatics program
• running scripts

Objectives: After this course you should be able to:

• navigate and use common commands in unix shell
• download specific gene sequences or genomes from NCBI (even with a big list of gene sequences)
• create use these genes as a database to annotate a sequencing dataset
• estimate the number of genes and their corresponding annotations in multiple sequencing datasets

Related courses:

• Introduction to RNA-seq and ChIP-seq data analysis
• Analysis of high-throughput sequencing data with Bioconductor