Peak Calling

Overview

This skill automatically performs core peak calling with MACS2 for ChIP-seq and ATAC-seq data, based on the BAM files in the current directory. It includes automatic experiment recognition and parameter selection.

Main steps include:

• Refer to the Inputs & Outputs section to check inputs and build the output architecture. All the output file should located in ${proj_dir} in Step 0.
• Always prompt user for genome_size to use (e.g. hs or mm). Never decide by yourself.
• Always prompt user if required control files are missing for ChIP-seq data.
• Always prompt user for the q value cutoff for peak calling.
• Detect experiment type (TF, histone mark, or ATAC-seq).
• Automatically decide whether to call narrow or broad peaks.
• Always use filtered BAM file (filtered.bam) if available.
• Detect sequencing type (single-end or paired-end) using SAM/BAM flags.
• Perform MACS3 peak calling accordingly.
• Generate a parameter log file (${sample}_used_parameters.txt) with justification for each chosen option.