What are the untrusted regions?

Untrusted regions (also called low quality ends or region of untrusted bases or bad ends) are clusters of bases at one or both ends of your sample that cannot be trusted because they are low quality (ambiguous). These regions appear in DNA Baser highlighted in gray color - see screenshot below. DNA Baser automatically detects these regions (see “Trimming engine”) and “trims” them from your sample which means that these regions will be ignored when sequence assembly is performed. Please note that the untrusted bases are not actually deleted from your sample. They are rather ignored.

Fig 1 - Untrusted region of bases highlighted in gray color.

How can I edit bases or define untrusted (low quality) regions.

Chromatogram Explorer v3.0 allows you to manually or automatically (batch) trim low quality ends. It will not allow you to edit the bases. However, with DNA Baser you can edit the bases (without performing sequence assembly).
This article shows how to mark bases as trusted/untrusted.

In my sample, I want to manually define low quality regions and save them to disk.

The information about untrusted regions cannot be saved to disk. Simply put, the FASTA, ABI, SCF format does not support this. “Gray regions” (untrusted bases) is a unique feature offered by DNA Baser! The regions are gray only inside DNA Baser. Once you close DNA Baser, this information is lost. The program redetects untrusted regions next time you reload that sample by reapplying the trimming engine algorithm. However, it cannot detect/remember which bases you have manually defined as gray (untrusted) in a previous session. Again, this is because ABI/SCF format cannot store this information.

The only way to keep your sequence trimmed after saving them to disk is to actually delete the gray (low quality) regions.
To do this, please follow these steps:

1) Start DNA Baser and load your sample(s). To do this double click your sample in Project Manager or drag your sample(s) from Windows Explorer in DNA Baser.
2) Manually delete the low quality regions by selecting the bases you want to delete then pressing the Delete key. In most cases, DNA Baser will automatically detect and mark in gray color the low quality ends you may want to delete.
3) If necessary, edit your bases.
4) When done, save your sample back to disk: in the File menu, choose 'Save sample as...', then choose 'SCF' if you want to keep your chromatogram (recommended) or FASTA.

Details about chromatogram files

• What is a chromatogram
• What is a good chromatogram
• FAQ about quality values (QV)
• Automatic low quality ends trimming