homer-motif-analysis

To find over-represented transcription factor binding motifs in ChIP-seq peak sets, you need de novo motif discovery. This Skill uses the HOMER suite to identify enriched sequence patterns and annotate genomic peaks with nearby genes.

Yes, you can perform known motif enrichment analysis on ATAC-seq data. This Skill supports ATAC-seq peak sets to check if your regions match known transcription factor binding motifs from established databases.

The best way to annotate genomic peaks with promoters and nearest genes is through peak annotation. This Skill assigns genomic features like promoters and introns to your peaks, revealing potential regulatory targets.

Yes, this motif discovery workflow supports the hg38 genome. You can run both de novo and known motif discovery directly on your ChIP-seq or ATAC-seq peak files using the hg38 reference genome.

Yes, you need pre-processed genomic peak files for transcription factor binding site identification. This Skill takes peak sets as input to discover enriched DNA sequence patterns and identify active regulatory regions.