How to use DNA Baser
Part 1

How to assemble two chromatogram files

 





Level: beginner

     This tutorial will show you how to assemble contigs from chromatogram/fasta/seq files.

During the assembly the following steps are automatically performed:

- cleaning of the bad ends
- assembling into a contig
- error correction
- vector removal using primer sequences (if option is checked)

1. Open DNA Baser by clicking its icon on your desktop. When DNA Baser starts, the Project Manager should be opened by default. Navigate to the folder where your files are.

2. Open the Settings window and navigate to the Assembler engine tab. Here you can choose the parameters for assembling the contig, trimming the bad ends of the chromatograms and mismatch (sequencing error) correction.

3. Select the primers you want to use for the removal of contaminant vector sequences. Click here to read how to do this.

4. Next step is to choose a name for this current project. DNA Baser will automatically choose a name for you but you can change it. Use this box to choose/change project's name:

5. Select two or more files that are going to be assembled by adding them to the JOB LIST. DNA Baser supports SCF, ABI, FASTA and SEQ.

You can add files to the Job List in several ways:

-use the button to add selected file/files to the Job List.
-use the button to add all files to the Job List.
-using your mouse, drag and drop files one by one from File List to the Job List.
If you want to remove files from the Job List, than use button.
6. The final step is to press the START button. In this moment, DNA Baser should begin the assembling process.

If something is wrong, the START button will be disabled:
This can be caused by:
-less than 2 files in the Job List
-invalid combinations of file types in the Job List
-one or more files in the Job List are invalid or it has been removed from your computer's hard disk meanwhile.
7. After the assembly process, you can check the log file. If DNA Baser has not already showed the log window for you, then press this button to display it.

8. The assembled sequence, the corresponding chromatograms and the consensus contig are displayed in the assembly window (click here if you want to know more about the assembly window).

Read the next tutorial to find out how to edit, remove vectors and save the assembled contig. If you have any questions, don't hesitate to write an email to us or to use our forum for support.