Table 1.

Files generated by MACS for the HudsonAlpha Institute FoxA1 dataset

File Name	Description
HAIB_T47D_FoxA1_model.r	An R script for producing a PDF illustrating the peak model
HAIB_T47D_FoxA1_model.pdf	The PDF image of the read distribution in model peaks and fragment size estimation, which is available only after executing Step 6Av
HAIB_T47D_FoxA1_peaks.xls	Key parameters used by MACS and detailed information of every peak identified by MACS
HAIB_T47D_FoxA1_peaks.bed	Peak locations in BED format
HAIB_T47D_FoxA1_peaks.subpeaks.bed	Subpeak locations in BED-like format. This file is generated by PeakSplitter, which is called by MACS
HAIB_T47D_FoxA1_summits.bed	Summit locations of the peaks in BED format
HAIB_T47D_FoxA1_MACS_bedGraph	Directory where the BedGraph files are generated. For each control or ChIP-seq sample, a BedGraph file describes the read distribution along the whole genome