PEPATAC glossary

Information regarding universal ATAC-seq terms and definitions are available from the ENCODE consortium.

Additional information relevant to PEPATAC output and interpretation includes:


Peak calling output

The pipeline's default peak caller is MACS2. More detailed descriptions regarding MACS2 output may be discovered in the MACS2 repository.

The following files are included in default PEPATAC analyses:


QC output


Signal tracks

The tool to produce these tracks, bamSitesToWig.py, is included in the PEPATAC repository and may be called indpendently with parameters like the --smooth-length further customized.