1.4. How can I view trace data in the Workbench?
Trace data associated with sequences can be viewed when working with sequence lists or stand alone read mappings in the CLC Workbenches.
Trace data cannot be viewed within track-based data types.
Trace data can be viewed, while running unlicensed CLC Workbenches using the View Mode. In contrast trace data could not be viewed in the now discontinued free CLC Sequence Viewer.
- The importer to use when importing data with trace information
- Viewing traces in a sequence or sequence list
- Viewing traces in a stand-alone read mapping
- Viewing traces for track-based mappings
The Standard Importer brings in the trace information. The NGS Sanger importer does not.
Traditional Sanger sequencing data should be imported using the standard import option. In the CLC Genomics Workbench this importer is found at
Import | Standard Import
The CLC Genomics Workbench import option Import | Sanger is designed for import of large, NGS-scale, data sets and removes trace information. If you want to retain trace data this is NOT the importer to use. This Sanger data importer is explained in further detail in the user manual here:
To view trace information for sequences, either a lone sequence or sequences in a sequence list, open the sequence or sequence list in the viewing area and use the viewing options, usually found at the right hand side of the viewing area. Open the section called Nucleotide info and check the relevant options under the Trace data section, as shown in the image below.
This, and more details about the Nucleotide info view settings, can be found in the manual at :
The same information presented above for viewing trace data is relevant if you have mapped Sanger reads to a reference and you wish to view the trace data in a resulting stand-alone mapping object. Here, one additional step is necessary:
- Under the Read Layout section, the Compactness is set to Not compact
- As described above, under the Nucleotide Info section, the option to view the Traces is checked and all the base traces are checked.
Trace data associated with reads in reads tracks, that is track-based mappings, cannot be viewed while in track format.
To view trace information for such reads within the mapping, please convert the reads track (track-base mapping) to stand alone format using the tool:
Toolbox | Track Tools | Convert From Tracks
Then use the information above about viewing traces in a stand-alone read mapping.