The recommended organization for a Phrap assembly is as follows:
•The .ace file is in a folder named EDIT_DIR
•The trace files are in a sibling folder named CHROMAT_DIR
•The .phd files are in another sibling folder named PHD_DIR
If you have not followed this convention, then SeqMan Pro will prompt you to locate the first trace file. The .phd files will be in the same folder as the trace files unless you have explicitly chosen another location for them or have chosen not to create them. If they are not in the same folder, SeqMan Pro will prompt you to locate those files, as well. Once a trace or .phd file has been found, all other trace or .phd files in the same folder(s) will be found automatically.
When queried for a file location, you may choose Skip to cancel the search for a particular file or Stop to cancel the search for all trace data in the project. If you choose Stop, the sequence data will still be available when your project is opened.
Note: As long as an .ace file is available, sequence and alignments can be viewed, but if some constituent .phd files are not found, those sequences’ trace files will not be available in the Alignment View.