Finding experiments and reads from SRA/ENA

The Short Read Archive (SRA) and the European Nucleotide Archive (ENA) are databases of records of raw high-throughput-DNA sequence data. Each is a mirrored version of the same sets of high-throughput sequence data, submitted by scientists in all fields of biology from all over the world. The free availability of high-throughput sequence data through these databases means that we can conceive of and execute new analyses on existing datasets. By performing searches on the databases, we can identify sequence data that we may wish to work with. In this recipe, we'll look at using the SRAdb package to query the datasets on SRA/ENA and retrieve the data for selected sets programmatically.

Getting ready

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