Automatic bad end trimming

       Why my are alignments wrong? Why are my blast hits totally crazy?

       The problem with wrong alignments or false blast hits often appears when the bad ends of the chromatograms have not been properly cleaned.

       DNA Baser is doing the cleaning automatically in each of the following 2 cases:

       - from single sequences when they are opened in the editing window
       - from contigs, during the assembly process

       How is DNA Baser cleaning the bad ends of the sequences:

       The end trimming process is based on the quality values which are assigned to each base. The bases are removed when their quality values are lower than a threshold quality value, which is set by the user. Beside the threshold quality value, there are 2 more parameters for end trimming: the length of the trimming window and the percent of bases in the trimming window whose quality values are higher than the threshold one.

See also:

      - About quality values (QV)
      - What is a good chromatogram?