HOMER De Novo Motif Discovery

Overview

This skill enables comprehensive de novo motif discovery using HOMER tools for genomic peak files. It discovers novel transcription factor binding motifs from genomic regions without requiring prior knowledge of motif patterns. To perform de novo motif discovery:

• Always refer to the Inputs & Outputs section to check inputs and build the output architecture.
• Genome assembly: Always returned from user feedback (hg38, mm10, hg19, mm9, etc), never determined by yourself.
• Check chromosome names: Standardize chromosome names to format with "chr" (1 -> chr1, MT -> chrM).
• Set analysis parameters: Region size, number of motifs, motif lengths
• Run HOMER de novo motif discovery command

When to use this skill

Use this skill when you need to uncover sequence motifs enriched in the promoter regions of a set of genes, or directly from a set of genomic regions, such as peaks from ChIP-seq or ATAC-seq, without prior assumptions about which transcription factors are involved. Typical use cases include: