Skip to content

GIFTwrap Commands:

  1. giftwrap: The main command for processing GIFT-seq data that runs the full pipeline end-to-end.
  2. giftwrap-count: Command for manually counting GIFT-seq data from FastQ files.
  3. giftwrap-correct-umis: Command for manually correcting UMIs in GIFT-seq data.
  4. giftwrap-correct-gapfill: Command for manually correcting gapfill sequences in GIFT-seq data.
  5. giftwrap-collect: Command for manually collecting GIFT-seq data after processing.
  6. giftwrap-summarize: Command for manually performing basic QC on GIFT-seq data after collection.
  7. giftwrap-generate-r: Command for generating an R script backbone for importing GIFT-seq data into Seurat. See the Seurat integration tutorial for more information on how to use this command.
  8. giftwrap-generate-tech: Command for generating a scaffold for a new GIFT-seq technology design. See the Extending GIFTwrap tutorial for more information on how to use this command.
  9. giftwrap-convert-probes: Converts a 10X Cell Ranger probe set to a GIFTwrap-compatible probe set file.
  10. giftwrap-revert-probes: Converts a GIFTwrap-compatible probe set file to a 10X Cell Ranger probe set. This can be useful for comparing to ranger-processed data.