CSC

Editing Techniques

• Consensus and Quality Cutoffs
• Editing by Base Change or Confidence
• Base overcalls
• Base undercalls
• Multiple Base Disagreements
• Poor Quality
• Checking for Errors

The editor documentation describes the available controls, but not how these should be used most efficiently. Some editing is performed in a local style or is personal preference, but a great deal of the common editing tasks are best dealt with in specific ways. This section aims to give example methods of resolving the common problems. Typically, problems will be found using one of the editor searches (such as "consensus quality" or "problem"). Used in conjunction with "Auto-display traces" (see section Trace Display Settings) this will automatically bring up a set of traces that are likely to be of assistance in resolving the problem. Prior to working on a contig it can be helpful to use "Shuffle Pads" to try to align padding characters See section Shuffle Pads.