You must select a name and location for your project in the Assembly Output dialog before proceeding further in the wizard. The dialog below is shown for all workflows other than the de novo or special reference-guided workflows. However, the “Additional files” options described below are only available for the templated transcriptome/RNA-Seq workflow.
Note: For de novo or special reference-guided workflows, see Assembly Output (De Novo, Special Reference-Guided).
•Project name – Enter a name for all output files, including the finished assembly. The finished assembly will be saved in BAM format.
•Project folder – Use the Browse button to select a location for your assembly output files.
o For non-Cloud assemblies, Browse launches your file explorer. Navigate to the desired location and then click Open to exit. The required disk space may range from 1 GB to 5 TB, depending on a variety of factors. See our technical requirements page for more information.
Note: Never save the assembly output files directly to the desktop, as the many intermediate files and folders created during assembly may hamper or prevent further computer operations. However, files may be saved to a folder on the desktop.
o For Cloud assemblies,
Browse opens the DNASTAR Cloud Data Drive and displays your files on the
DNASTAR Cloud. Navigate to the desired location and highlight the target folder,
then click the green check mark (
) to exit from the DNASTAR Cloud Data
Drive.
The Assembly output display shows the output file name with its extension, based on the workflow and the selections made above.
•SeqMan Pro Format – (Sanger Validation workflow only) Check this box to save the assembly in SeqMan Pro format (.sqd). Even if the box is checked, the assembly will only be saved in this format if is 10 million reads or less.
•Additional Files – This section appears only if you are following the templated transcriptome/RNA-Seq workflow. Select additional output files to create during assembly:
o None – To create no additional output files.
o WIGGLE files – To create WIGGLE (.wig) files. The saved WIGGLE files contain coverage data, with a separate file for each chromosome. These files are written to a separate folder called assembly_name-wiggle, which can be found in the same location as the .assembly and reports folder.
In DNASTAR’s GenVision Pro, WIGGLE files can be added as tracks in order to view the data as coverage plots. Note that these coverage plots will typically match the coverage tracks generated automatically when the assembly is opened with GenVision Pro.
Note: The QNG assembler used for RNA-Seq assemblies is designed to export a WIGGLE file of the targeted feature areas only (i.e., the coverage actually used in measuring the peak). Introns and untranslated regions are not included. Because of this, the WIGGLE files that are output during SeqMan NGen assembly may not match the number of sites found visually using SeqMan Pro.
o Take mean of every ‘n’ bases – Input the number of bases on which the mean number of RNA-Seq counts should be estimated.
•Save Script – Press this button if you wish to save your project and convert your wizard choices into a SeqMan NGen assembly script (.script) prior to assembly. (A copy of the script is saved automatically when you initiate an assembly from the “Your assembly is ready to begin” screen.) This button is not available for Cloud assemblies. The resulting assembly script is an editable text file that can be modified and re-run if desired.
Note: If you use Save Script after having checked the Run as separate assemblies box in the Input Sequence Files and Define Experiments or Individual Replicates screen, a set of three separate scripts will be saved for the project. If you save one or more of these scripts to a location other than the main project folder, any attempt to run the assemblies from the SeqMan NGen project script will fail. Moving the projects back to the main project folder will allow assembly to proceed.
•Write log file – To create and save a log file that can be used for troubleshooting any issues with the assembly.
Once you are finished, click Next > to continue to the next wizard screen.
Note: If you choose a name that already exists in the chosen location, you will receive the following warning. Click OK to continue and over-write the earlier project; or Cancel to return to the wizard screen, where you may change the project name and/or location.
