discover-motifs

Prepare or run de novo motif discovery from candidate footprint intervals or an existing FASTA file.

Example command

discover-motifs --candidates project/samples/sample/footprints/sample_candidate_footprints.bed --genome hg38.fa.gz \
  --flank 75 --method streme --known-motif-db jaspar2026_vertebrates --outdir project/de_novo/sample --execute

Primary inputs

• --candidates — candidate-footprint BED intervals.
• --genome — reference genome used to extract candidate sequences.
• --flank — bases included on each side of a candidate center.
• --method — discovery method; the example uses STREME.
• --known-motif-db — optional known-motif database for Tomtom matching.
• --outdir — directory for candidate FASTA files and discovery results.
• --execute — run discovery immediately using the managed MEME Suite runtime.

Main outputs

{outdir} is the selected discovery directory:

Path	Meaning
{outdir}/candidate_sequences.fa	Reference sequences extracted around candidate footprint intervals.
{outdir}/run_motif_discovery.sh	Reproducible MEME/DREME/STREME command plan.
{outdir}/{method}/streme.txt or the method-equivalent MEME output	De novo motif models when --execute is used.
{outdir}/tomtom/tomtom.tsv	Optional similarity matches to the selected known-motif database.
{outdir}/motif_summary.tsv and motif_summary.html	Summary targets written by the generated plan after discovery and matching complete.

Continue with summarize-motifs, or see the complete discover-motifs reference.