Extract sequences from tracks

Note that the functionalities described in this page are valid for sequence or reads tracks. For similar functionalities on read mappings, see Extract reads from a mapping.

Extracting the sequence from a sequence track

It is possible to extract a DNA sequence from a sequence track included in a Track List with the Extract Sequence... option of the right-click menu on the sequence (menu to the right of figure 24.11). In this case, a pop up window proposes to Extract annotations, which will extract all the annotations present on the other tracks of the Track list, and add them to the extracted sequence.

Note that it is possible to extract the sequence of a single sequence track, but in this case (the track is not included in a track list), or when the sequence track is in a track list that does not contain annotation tracks, the option to Extract annotations is unavailable.

Extracting a single read/sequence from a reads track

Right-click on the sequence of interest and choose the Selected read... option to Copy, Open in a new view or Blast the selected sequence.

Extracting all reads/sequences from a track

Use the tool Extract Sequences from the Toolbox to extract sequences from the subset reads track as described in Extract sequences.

Extracting only selected reads/sequences from a track

The sequences of interest can be selected by dragging the mouse over the region of interest, followed by a right click on the reads (or on the sequences in the case of a sequence track) and a click on Create Reads Track from Selection (as can be seen on the menu to the left in figure 24.11).

Image extractsequence
Figure 24.11: Extract sequences from a read mapping track. This screenshot shows the menus available when right-clicking on the reference sequence and the sequences/reads in the tracks below.

An Extract from Selection pop up dialog lets you specify what kind of reads you want to include in the subset of the original reads track (figure 24.12).

Image extractsequence1
Figure 24.12: Selecting the reads to include.

Per default all reads are included. The options are: