Genomic Feature Annotation and Visualization with Homer

Overview

• Prepare genomic region files in BED or other supported formats. Ensure that the input genomic regions are provided in a valid BED format (chromosome, start, end). If the file does not meet this format, extract the required columns to create a valid BED file.regions file.
• Identify and specify the correct genome assembly for annotation.
• Always prompt user for the tool to use, choose from ChIPseeker or HOMER
• If the user choose HOMER, then:
  • Annotate the genomic regions using Homer's annotatePeaks.pl.
  • Generate annotation statistics and feature distribution summaries.
  • Visualize annotation results (e.g., pie charts, barplots).

When to use this skill