Working with Databases and Remote Data Sources

Large-scale model organism sequencing projects, such as the Human Genome Project (HGP), or the 1,001 plant genomes sequencing projects have made a huge amount of genomics data publicly available. Likewise, open access data sharing by individual laboratories has made the raw sequencing data of genomes and transcriptomes widely available, too. Working with this data programmatically can mean having to parse or bring locally some seriously large or complicated files. As such, much effort has gone into making these resources as accessible as possible through APIs and other queryable interfaces, such as BioMart. In this chapter, we'll look at some recipes that will allow us to search for annotations without having to download whole genome files and find relevant information across databases. We'll look at how to pull raw reads...