[DNA Baser-Manual-Editing] - Deleting a base form the contig. Deleting a base from a chromatogram.

Deleting bases in a sequence

Deleting bases in contig

These is a small difference between deleting bases in a chromatogram or in the contig: deleting a base from a sequence will simply remove that base. However, deleting a base from contig will replace that base with a GAP. This is necessary in order to keep the contig synchronized with the input sequences.

Deleting a base

The delete functions can be accessed in different ways:

from the Delete bases button in the main menu (see Fig. 1)
from the Delete bases button pop-up menu (right click a base to pop the menu as shown in Fig. 2)
pressing the DELETE key on your keyboard

NEW: Starting with DNA Baser v3 you can also delete a whole column.


Fig. 1 - The main menu	Fig. 2 - The pop-up menu (right click)

Attention

[Applies only if you edit bases in the assembly window]

In Assembly window, deleting bases from one of the assembled chromatograms will break the synchronization between that chromatogram and rest of the assembled chromatograms. DNA Baser will show a one-time-warning about this issue.

In addition, by deleting a base from one of the assembled chromatograms, you force DNA Baser to recalculate the contig. This means that all editing that you have done in contig (staring at the current deletion point and up to the end of the contig) will be lost. Because of this, we recommend you do make any deletion you want at the beginning and only when you are done deleting bases, you can proceed editing the contig.

To stay away from troubles, please avoid deleting bases, in order to keep the synchronization between sequences. Instead of deleting a base, you may want to replace it with a GAP.

Hints

You can delete a single base (the base under the cursor) or all selected bases.
To edit a single sequence, double click that sequence in Project Manager to load it. Multiple sequences can also be easily edited in the Assembly window.
In Assembly window, you may want to replace a base with a GAP instead of deleting it.

EXAMPLE - Deleting 20 bases at once:

In the screen shot below, you can see that bases numbered from 60 to 80 highlighted (yellow marker). By pressing the Delete bases, DNA Baser will delete all marked bases at once. This operation can be applied on chromatograms but also on the contig.