Loop Annotation

Overview

This skill performs loop annotation for Hi-C/HiChIP/ChIA-PET interaction data. It identifies regulatory and structural loop types (E–E, E–P, P–P, CTCF-CTCF).

Main steps include:

• Refer to Inputs & Outputs to verify necessary files.
• Always prompt user if required files are missing.
• Always prompt user for genome assembly used.
• Build enhancers.bed if absent (ATAC + H3K27ac).
• Build promoters.bed if absent (.tss annotation).
• Always prompt user for the column index of the interaction count in the raw BEDPE file. Never decide by yourself.
• Standardize the format of the .bedpe file as the input of annotateInteractions.pl
• Run annotateInteractions.pl with feature sets.
• Visualization