Export of folders and data elements in CLC format

The CLC Genomics Workbench stores data in CLC format. A CLC format file holds all the information for a given data element. This means the data itself, as well as information about that data, like history information.

Data can be exported in CLC format by selecting the CLC fomat, or the zip format, from the list of available formats.

If CLC format is chosen, each selected data element can be exported to an individual file. An option is offered later in the export process to apply gzip or zip compression. Choosing gzip compression at this stage will compress each data element individually. Choosing zip produces a single file containing the individual CLC format files. If a single zip file containing one or more CLC format files is the desired outcome, choosing the zip format in the first step of the export process specifies this directly.

If a folder is selected for export, only the zip format is supported. In this case, each data element in that folder will be exported to CLC format, and all these files will be compressed in a single zip file.

CLC format files, or zip files containing CLC format data, can be imported directly into a workbench using the Standard Import tool and selecting "Automatic import" in the Options area.

Backing up and sharing data

If you are backing up data, or plan to share data with colleagues who have a CLC Workbench, exporting to CLC format is usually the best choice. All information associated with that data element will then be available when the data is imported again. CLC format is also recommended when sharing data with the QIAGEN Bioinformatics Support team.

If you are planning to share your data with someone who does not have access to a licensed CLC Genomics Workbench but just wishes to view the data, then you may still wish to export to CLC format. A CLC Genomics Workbench can be run without a license in Viewing Mode, and CLC format data can be imported in the same way it would be using a licensed Workbench. Viewing Mode is described further in Viewing mode.

Compatibility of the CLC data format between Workbench versions

When exporting to CLC or zip format, an option called Maximize compatibility with older CLC products is presented at the Specify export parameters step, as can be seen in figure [*]. With this option checked, data will be exported without internal compression. Data exported with this option turned on may be larger than it would be otherwise.

Internal compression of CLC data was introduced in CLC Genomics Workbench 12.0, CLC Main Workbench 8.1 and CLC Genomics Server 11.0 using the LZ4 algorithm, a lossless compression method. This feature decreases the size of the data elements created by the software. However, CLC format files with internal compression are not compatible with older versions of the software. Thus, this option should be enabled when exporting data intended for use with older CLC software versions.

Internal compression is not required for compatibility with Workbench versions released after this feature was introduced. In other words, data generated in older Workbench versions can, in general, be imported into newer Workbench versions. We endeavor to maintain backwards compatibility of CLC format files whenever possible, so that most CLC format files made using an older version of a Workbenches can be imported into newer Workbench versions.

Internal data compression can be turned off, so no data created is internally compressed. How to do this is described in the Workbench Preferences documentation Data Compression.