Peak Calling

DRAGEN calls peaks using an algorithm based on MACS, version 3 (Zhang et al., 2008)¹. To customize the behavior of the peak calling algorithm, modify any of the command line parameters specified in the table below.

Command line parameter	Meaning	Default value
atac-peak-qvalue	Threshold for q-value to call peaks	0.05
atac-peak-fold-change	Fold change threshold (relative to the background) to call peaks	1.0
atac-peak-min-length	Minimum length of a peak, bp	200
atac-peak-max-gap	Maximum pileup gap (if the gap is larger - initiate another peak), bp	50

Alternatively, if fragment counting needs to be performed on a pre-specfified set of peaks, provide a peak BED file using command line parameter atac-peak-bed-file.

¹Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown M., Li. W. and Liu, X.S., 2008. Model-based Analysis of ChIP-Seq (MACS). [PDF] Available at: <https://pubmed.ncbi.nlm.nih.gov/18798982/> [Accessed 1 March 2022].