Menu Command

Description

Summary

To make the Project Summary window active.

Statistics

To open the Project Statistics report.

Report

To open the Project Report window.

Trim Report

To open the Trim Report.

Parameters

To view and/or edit your project parameters.

Vector Catalog

To access the Vector Catalog.

Contaminant Seqs

To open the Contaminant Sequences window.

Repetitive Seqs

To open the Repeated Sequences window.

Empty Report

To clear the Project Report. Edit > Undo will not restore the contents of this report, so only do this if you are sure you do not want this information in your assembly document.

Empty Trim Report

To clear the Trim Report. Edit > Undo will not restore the contents of this report, so only do this if you are sure you do not want this information in your assembly document.

Update

To open a submenu of commands allowing you to choose from the following tasks:

•      Find Moved Files—SeqMan Pro will try to locate the original files that were used to assemble the current project, and then moved after project assembly. If SeqMan Pro can locate the files, no further action is necessary. If the files cannot be found, SeqMan Pro will open a Find dialog and ask you to locate them.

•      Update Trace Weights—Updates trace weights and evidence scores. To update pre-Lasergene99 projects, or projects with corrupted weights. SeqMan Pro displays alerts if the trace files are unavailable or if a project has already been updated.

•      Attach Trace Data—Attaches original trace data to a project. This option greatly increases the size of project document.

•      Remove Trace Data—Removes any trace data attached to the project. Use of this command shrinks the size of the document.

•      Update Paired-End Pairs—Updates the pair info in the project.

•      Compact Project—frees up disk space without affecting any data. This command is good for shrinking projects from which many sequences have been deleted or upon which the Remove Trace Data option has been applied.

Create New Scaffold

Ctrl/Cmd+K

To create contig scaffolds.

Order Contigs

To arrange contigs into scaffolds and order them within each scaffold utilizing available paired end data.

Place Unlocated Contigs

To place assembled contigs from the unlocated contigs group into existing scaffolds using mate pair data. New scaffolds will also be created when justified by the mate pair information. You will receive a confirmation prompt before ordering takes place. Click Order to continue.

If no pairs were found, the following message will be shown:

In either case, the Report window will open to show the results of ordering.

Show Coverage of Targeted Regions

To open an Exome Coverage (.bed) file as a Coverage of Target Region [x] report.

Genetic Code

To select a genetic code or to modify the list of genetic codes.

Edit Genetic Code

To alter the selected genetic code.