Scan genomic regions for transcription factor motifs using HOMER.
npx skills add https://github.com/BIsnake2001/ChromSkills --skill motif-scanning
Please help me install this Agent Skill. Skill: motif-scanning Source: https://github.com/BIsnake2001/ChromSkills/tree/main/14_toolBased.known-motif-scan Command: npx skills add https://github.com/BIsnake2001/ChromSkills --skill motif-scanning
Identifies exact locations of known transcription factor motifs within experimental genomic regions such as ChIP-seq or ATAC-seq peaks, enabling interpretation of regulatory elements.
Provide your peak file and genome assembly to run HOMER motif scanning and save results.
High-intent search queries and answers about installing and using this skill.
To find known transcription factor motifs in ATAC-seq peaks, use HOMER motif scanning to identify exact motif locations within your genomic regions. Provide your peak file and genome assembly to detect occurrences.
HOMER motif scanning supports standard peak formats including BED, narrowPeak, broadPeak, and HOMER peak files. You provide these files along with your target genome assembly to locate transcription factor motifs.
Yes, you can scan for transcription factor motifs in ChIP-seq peaks using the hg38 genome assembly. The process supports multiple assemblies including hg38, mm10, hg19, and mm9.
Locating known motifs in genomic regions produces motif-hit lists and optional BED or annotation outputs. These outputs enable downstream visualization and co-factor motif analysis within your HOMER workflows.
You must specify a genome assembly for motif scanning because the tool uses position-specific scoring matrices from known motif databases mapped to that specific genome sequence to accurately detect transcription factor motif occurrences.
BIsnake2001Identify enriched transcription factor motifs in genomic regions using HOMER.
BIsnake2001Identify known transcription factor motif enrichments in genomic peak regions using HOMER.
jaechang-hitsDiscover de novo motifs and annotate genomic peaks with HOMER.
AlterLab-IEURetrieve JASPAR transcription factor binding profiles and scan DNA sequences for motif sites.
