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Visium custom probes

Visium: Custom Probes

Data Type

When analyzing Visium Spatial Transcriptomics data which has been prepared using custom probes, the reference genome must be combined with those probes prior to running that analysis.

Steps:

  1. Upload the custom probe(s) as a "Nucleotide Sequences (FASTA)" dataset (either in a single or multiple files)
  2. Open the "Build SpaceRanger Reference" pipeline and select the uploaded probes
  3. Select the appropriate reference genome (human or mouse) to combine with those probes
  4. Provide a memorable name for the custom reference and click "Run"
  5. Once the custom reference is finished building, it can be used with the "Visium Spatial Transcriptomics (Custom Probes) pipeline
Technical Details

Workflow Repository: github.com/FredHutch/nf-cellranger-tools

Citations: