Downloading reads and metadata from SRA

Click on Download Reads and Metadata to save reads and their associated data. The data is saved in a metadata table and can be later associated to the reads for use in downstream analysis, for example to define factors for differential expression in the Differential Expression for RNA-Seq tool. Should the metadata table later be deleted, the "Show Metadata for Selection" button can be used to quickly recover a copy without having to re-download all the runs.

The Download Reads and Metadata wizard offers the following options:

Import Options

(figure 7.3)

Image srasearchimport
Figure 7.3: The Download Reads and Metadata Import Options dialog.

As with other NGS reads importers, it is possible to discard read names and/or quality scores to save space.

Edit Paired End Settings

(figure 7.4)

Image srasearchpaired
Figure 7.4: The Download Reads and Metadata Edit Paired End Settings dialog.

This dialog appears for all runs marked as being Paired (Paired column contains "Yes").

Read orientation is always guessed to be "Forward Reverse" unless otherwise stated.

Minimum distance and Maximum distance depend on how much data the depositor supplied with the runs. They are allowed to supply an "Insert Size" and an "Insert Deviation".

When possible, we generally recommend that SRA data be used in subsequent analyses with the "Auto paired end distance detection" option enabled as the quality of deposited information is low. For example, some depositors report insert size including the length of the reads, and some excluding the length of the reads.