Convert Metadata to Cell Annotations

Metadata is often present at both the sample and cell level. However, it is always possible to convert sample level metadata into cell level metadata. For example, the knowledge that a sample comes from `Lab A' can be captured by annotating the entire sample with `Lab A', or alternatively by annotating all the cells in the sample with `Lab A'.

For simplicity, most tools in the CLC Single Cell Analysis Module only accept cell level metadata. Convert Metadata to Cell Annotations is provided to easily transform sample level metadata in the form of Metadata Tables (see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Metadata.html for more details) into cell level metadata in the form of Cell Annotations. Convert Metadata to Cell Annotations can be found in the Toolbox here:

        Utility Tools (Image sc_utility_tools_folder_open_16_n_p) | Convert Metadata to Cell Annotations (Image convert_metadata_to_cell_annotation_16_n_p)

The tool can take an Expression Matrix (Image expression_matrix_track_16_n_p) / (Image expr_matrix_spliced_unspliced_16_n_p), Velocity Matrix (Image velocity_matrix_16_n_p), or Peak Count Matrix (Image peak_count_matrix_16_n_p) as input and produces a single Cell Annotations (Image cell_annotations_16_n_p) element. An example of this process is shown in figure 14.1.

Image sampletocellmetadata
Figure 14.1: A Metadata Table (left) annotates a sample as being produced by `Lab A' on `11.12.2010'. Convert Metadata to Cell Annotations converts this metadata into Cell Annotations (right) where each cell in the sample is annotated with the same information.

The tool does not require the sample level metadata to be explicitly provided. Instead:

In a workflow
the sample level metadata is taken from a Metadata Table provided to the workflow, if present.
Otherwise
the sample level metadata is collated from all the Metadata Tables that reference the input Expression Matrix. If multiple such tables exist, their annotations are combined. If the annotations are in conflict, for example one table says the sample has `Lab = Lab A' and another says `Lab = Lab B', then the Lab will be missing (and hence unknown) in the combined table. Note that after connecting to a CLC Server, additional metadata tables, only present on the server, may be found by the tool.