Working with projects

A project file ('.BaserProj') contains a copy of your input files (including the reference), the contig file and the log file.

Loading a project

To load an existing project, you can:

• press the 'Open project' button under the 'File' menu
• double click a project file in Windows Explorer
• double click a project file in Sample Explorer

Saving a project

DNA Baser automatically chooses a name for your project and it will automatically save the project to disk when you press one of the 'Start contig assembly' buttons. This behavior can be change in 'Auto Save' box located under 'Project options' tab.

IMPORTANT NOTE ABOUT WRITE PERMISSIONS

 

Please make sure that DNA Baser has write permissions to the output folder, else it won't be able to automatically save the project and the contig to that folder. This is a pretty common mistake if you are working with Windows Vista or 7 as these two operations system tend to lock access to system folders (such as Windows and Program Files) and to folders created by other users. It can also happen often in a corporate environment where the network administrators deny write access to all kind of folders (especially shared/network folders).

Therefore, if you see a specific error message after you press the 'Start assembly' button probably it means that your input samples are already in a folder without write permissions. As by default DNA Baser tries to save the project/contig in the same folder where the input files are, you get an error message.

If you made changes into the project (you added/removed samples, edited bases in the contig or in the assembled samples, etc) you need to save the project to disk. To do this, press the 'Project -> Save project' menu or Control+S.

Saving the contig

DNA Baser will automatically save the contig to disk at the end of the assembly process. This behavior can be change in 'Auto Save' box located under 'Project options' tab. The contig is saved as SEQ, TXT or FASTA, depending on what the user has chosen in the 'Project options' tab.

Contig name

The contig file will have a name similar to project's name but it will start the word 'Contig' (this behavior can be changed in 'Project options' tab). This will help the user to easily identify the new generated contigs file among other files.

For example, if you project name is 'C:\MySamples\EColi.BaserProj', then your contig name will be 'C:\MySamples\Contig - EColi.Fasta'.

If you made changes into the contig (you added/removed samples, edited bases in the contig or in the assembled samples, etc) you need to save the contig to disk. To do this, press the Contig -> Save contig' menu, by pressing the Control+Shift+S key combo or by pressing the FINISH button.

Overwriting your original sample files

Please note that when you build a project (for sequence assembly or batch sequence assembly), DNA Baser will create a copy of your input files. All edits performed in the Assembly Grid are applied only to the copy. Therefore, your original files will remain unaltered!

The only way you can alter your original files is to press the 'Save sample' or 'Save sample as' buttons under the 'Sample' menu and overwrite the input files.

Adding/removing samples

To add or delete samples from an existing project use the 'Project->Add new sample' and 'Remove sample' menu.