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

Deleting bases

Deleting bases in the input sequence

Deleting bases in the contig

IMPORTANT

DNA Baser is different than other sequence assemblers you may be used to. Even though it is quite easy to delete a base (by pressing the Delete key) you can edit the alignment or clean low quality bases (at the end of the chromatograms) without actually deleting any bases. It may seem a bit awkward in the beginning but after using it few minutes you will see its advantage.

How to delete low quality bases at the end of the chromatograms?

You don't! DNA Baser is different than other sequence assemblers you may be used to: DNA Baser automatically detects low quality regions in your input files and mark those regions in gray color so they are not taken into consideration while building the contig.

In the low probability that you are unhappy with the way it detected the low quality regions, please adjust the Trimming Engine parameters and reassemble your contig. If you really really need to take manual control over this, you can easily do it: in the assembly window highlight the region that you want to 'cut' then right click it. In the pop-up menu choose 'Mark region as untrusted'. That's it. DNA Baser will rebuild the contig and the region you just marked will not be taken into consideration anymore. You just eliminated some base without actually deleting them.

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

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)

The difference between deleting an input base & a contig base

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.

Forcing alignment (by shifting a sequence)

In the Assembly window, deleting bases from one of the input sequences will shift that sequence you can use this in extreme cases when you want to manually force a specific alignment.

Note: Shifting a sequence causes a synchronization break between that sequence and rest of the input sequences. DNA Baser will show a one-time-warning about this. Also, through this, you force DNA Baser to recalculate the contig. This means that edits that you have done in contig (staring at the current deletion point and up to the end of the contig) may be lost. We recommend you do make any deletion you want BEFORE making any edits in the contig.

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.