Note: This topic is not applicable to BAM-based projects.
If you wish, you may direct SeqMan Pro to proceed with all preassembly and assembly steps as soon as you drag and drop the folder of sequences on the Unassembled Sequences window.
To execute assembly and preassembly on drag and drop:
1) Organize your sequence files so that (a) all the files are in a single folder or tree of folders, and (b) no files other than the sequence files you want are in the folder or tree of folders
2) Launch SeqMan Pro. If you wish to change any parameters for trimming, screening, vector and assembling, do so now by accessing the Preassembling and Assembling parameters. Remember that, if you want vector trimming to occur, you need to specify a default vector.
3) Select Sequence > Add, then click Done—this opens an empty Unassembled Sequences window.
4) Launch Windows Explorer or Macintosh Finder and highlight the top-level folder containing your sequence data. Hold down Ctrl (Win) or Cmd (Mac) while using the mouse to drag the folder from Explorer/Finder to the Unassembled Sequences window in SeqMan Pro.
5) Once the folder icon is superimposed on the Unassembled Sequences window, release the mouse button. As you release the mouse button, a pop-up menu appears offering four choices:
Don’t Assemble simply adds the data, as happens when you perform a normal “drag and drop” procedure;
Trim & Vector Scan adds the data and trims the reads using the default vector (if set) and the default quality trimming options. This option does not execute the assembly step;
Assemble directs SeqMan Pro to perform all specified preassembly and assembly tasks without further intervention;
Expand Folders offers a submenu of the three choices above. You must use this option when you want to add sequences located in folders within the top-level folder you are dropping onto SeqMan Pro. If do not choose to Expand Folders, only sequence files located in the top level of the folder you are dropping will be added to your project.