Bioinformatics Data Skills

Chapter 6. Bioinformatics Data

Thus far, we’ve covered many of the preliminaries to get started in bioinformatics: organizing a project directory, intermediate Unix, working with remote machines, and using version control. However, we’ve ignored an important component of a new bioinformatics project: data.

Data is a requisite of any bioinformatics project. We further our understanding of complex biological systems by refining a large amount of data to a point where we can extract meaning from it. Unfortunately, many tasks that are simple with small or medium-sized datasets are a challenge with the large and complex datasets common in genomics. These challenges include:

Retrieving data

Whether downloading large sequencing datasets or accessing a web application hundreds of times to download specific files, retrieving data in bioinformatics can require special tools and skills.

Ensuring data integrity

Transferring large datasets across networks creates more opportunities for data corruption, which can later lead to incorrect analyses. Consequently, we need to ensure data integrity with tools before continuing with analysis. The same tools can also be used to verify we’re using the correct version of data in an analysis.

Compression

The data we work with in bioinformatics is large enough that it often needs to be compressed. Consequently, working with compressed data is an essential skill in bioinformatics.

Retrieving Bioinformatics Data

Suppose you’ve just been ...