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summarize-motifs

Turn completed motif-discovery results into a table of motif sequences, significance values, and optional matches to known motifs. Add an HTML report to review the results in a browser.

Example command

summarize-motifs --meme-txt project/de_novo/sample/streme/streme.txt \
  --tomtom-tsv project/de_novo/sample/tomtom/tomtom.tsv \
  --out-tsv project/de_novo/sample/motif_summary.tsv --out-html project/de_novo/sample/motif_summary.html

Primary inputs

  • --meme-txt — discovery output such as meme.txt, streme.txt, or dreme.txt.
  • --tomtom-tsv — optional Tomtom known-motif matches.
  • --out-tsv — compact output table for discovered motifs and matches.
  • --out-html — optional browser report.

Omit --tomtom-tsv if you did not run known-motif matching. This command reads existing results; it does not rerun motif discovery.

Main outputs

  • The --out-tsv file — tab-separated discovered motif IDs, consensus sequences, significance values, and known-database matches when available.
  • The --out-html file — optional portable HTML table containing the same summary and consensus-sequence logos when available.

Open motif_summary.html in a browser or import motif_summary.tsv into a spreadsheet. Known-motif matches help identify candidate TF families; they do not establish which TF is bound.

See the de novo motif discovery workflow and the complete summarize-motifs reference.