Importing data

The elements needed for executing the workflows can either be imported prior to the execution, or can be automatically imported during execution, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Launching_workflows_individually_in_batches.html.

For details on importers, see Data import.

If the workflow uses two different types of input elements, such as Expression Matrix (Image expression_matrix_track_16_n_p) / (Image expr_matrix_spliced_unspliced_16_n_p) and Peak Count Matrix (Image peak_count_matrix_16_n_p) or Expression Matrix (Image expression_matrix_track_16_n_p) / (Image expr_matrix_spliced_unspliced_16_n_p) and TCR Cell Clonotypes (Image cell_tcr_clonotypes_16_n_p) or BCR Cell Clonotypes (Image cell_bcr_clonotypes_16_n_p) element, the sample in the input elements must be the same for cells originating from the same sample. This can be achieved in different ways, depending on how the elements were generated:

Care must be take when executing a workflow in batch mode using on-the-fly import, as options that are explicitly supplied will be used for all imported files:

Image atac-rna-matrix-nearby-h5
Figure 20.4: Specifying nearby genes and transcription factors for HDF5 import.

Image atac-rna-matrix-nearby-mex
Figure 20.5: Specifying nearby genes and transcription factors for archive MEX import.