The peak format required by DiffBind is BED, whereas MACS2 does not output BED files as MACS14 (the earlier release) did. Rather, it outputs BedGraph (bdg) files, or a variant format of a BED file (see here: https://github.com/taoliu/MACS under Output Files), i.e., the *.narrowPeak or *.broadPeak files. How can this be resolved?

You can read in narrowPeak files by setting the PeakCaller to "narrow" in the sample sheet. Alternatively, you can read in the xls files created by MACS2 by setting the PeakCaller to "macs".

-Rory