Trimming Ends from the Alignment View

In the Alignment View, trim bars appear as black vertical bars on the left edge and small black triangles on the right edge of the sequence text.

•      To trim sequence ends, drag the trim bar toward the middle of the sequence using your mouse. The discarded portion of the sequence will disappear from view.

•      To restore formerly trimmed sequence ends, drag the bar away from the middle of the sequence. The double arrow of the cursor becomes a single arrow once the sequence is fully extended. By default, the restored sequence will be displayed on a yellow background. You can edit the color that SeqMan Pro uses for this by changing the Trimmed Color setting in the Editing & Colors parameters.

•      To trim the ends of multiple sequences simultaneously from the Alignment View, use the Sequence > Trim Ends command.

•      By default, .assembly file reads are not trimmed to the boundaries of the targeted regions defined by the .bed or manifest file. This can be changed by adding the SeqMan NGen scripting command trimToTargetRegions:true to the script and performing the assembly again.