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My platform is not in the supported list. Can I still use CartLoader?

Yes.
If your data platform is not one of the predefined platform options, you can still use CartLoader by converting your input into unified SGE format with:

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cartloader sge_convert --platform generic ...

How to apply CartLoader with unsupported platforms

  1. Prepare a transcript-level CSV/TSV with core fields:
  2. X coordinate
  3. Y coordinate
  4. feature name (typically gene)
  5. count (or one row per transcript)
  6. Run sge_convert in generic mode.
  7. Set CSV column names as needed using --csv-colname-x, --csv-colname-y, --csv-colname-feature-name, and --csv-colnames-count.
  8. Set spatial scaling using --units-per-um (or your equivalent known scale).
  9. Continue with standard downstream modules (run_ficture2, run_cartload2, uploads).

Example

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cartloader sge_convert \
  --platform generic \
  --in-csv /path/to/input.tsv \
  --csv-delim $'\t' \
  --csv-colname-x x \
  --csv-colname-y y \
  --csv-colname-feature-name gene \
  --csv-colnames-count count \
  --units-per-um 1 \
  --out-dir /path/to/out/sge

Notes

  • Start with a small subset first to validate formatting and scaling.
  • If your file has comments, delimiters, or headers that differ from defaults, set the corresponding --csv-* options explicitly.

See also: