Analysing Mapped Sequence Data with SeqMonk - TeSS (Training eSupport System)

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Bioinformatics and Biomathematics Training Hub

The Bioinformatics and Biomathematics Training Hub (BBTH) is a BBSRC-funded collaborative project to coordinate the development and sharing of training materials and expertise across the UK’s National Institutes of Bioscience (NIB — http://www.nib.ac.uk/) for the increasingly important areas of bioinformatics and biomathematics.

Guided by our NIB partners, researcher surveys, and interactions with interested bodies such as Elixir-UK, we will work to ensure that best use is made of existing assets and capabilities, that best practice is shared across the NIB, and that redundant effort is minimised going forwards.

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Analysing Mapped Sequence Data with SeqMonk

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SeqMonk is a program which can analyse large data sets of mapped genomic positions. It is most commonly used to work with data coming from high-throughput sequencing pipelines.

The program allows you to view your reads against an annotated genome and to quantitate and filter your data to let you identify regions of interest. It is a friendly way to explore and analysis very large datasets.

This course provides an introduction to the main features of SeqMonk and will run through the anlaysis of a couple of different datasets to show what sort of analysis options it provides.

Course content

What is SeqMonk
Starting and configuring the program
Creating a project and importing data
Using the chromosome viewer
Quantitating and Filtering Data
Creating Reports
Using Quantitation Pipelines
Correcting and Normalising Quantitations
Scaling analysis to larger studies
Running statistical tests
Interacting with external programs
Exporting text and graphics

Course Material

Licence: Other (Non-Commercial)

Keywords: Babraham Institute

Authors: Simon Andrews

Scientific topics: Sequence alignment