Motif Scanning

Overview

This skill enables comprehensive motif scanning using HOMER tools for genomic peak files. It scans genomic regions for specific transcription factor binding motifs using position-specific scoring matrices and identifies exact motif locations. To perform motif scanning:

• 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).
• Prepare motif files: Position-specific scoring matrices (PSSM) in HOMER format, saved in ${HOMER_data}/knownTFs/motifs/${tf}.motif, and "tf" should be in lower case.
• Set scanning parameters: Region size, score thresholds, output format
• Run HOMER motif scanning command

When to use this skill