ATAC DiffBind: use peak or summit file?

Question

[a_bis]

Hi all,

I'm trying to carry out a differential chromatin accessibility analysis on some ATAC-seq data using DiffBind. The programme requires the .bam file from each replicate, as well as a bed file of previously-called peaks (I used MACS2). The output from MACS2 is a summits.bed file, a peaks.narrowPeak file, and a peaks.xls file. As the analysis calls for a bed file of the peaks, should I be using the previously generated summits.bed file, or should I be reformatting/renaming one of the other two peak files (peaks.narrowPeak or peaks.xls) into a .bed file, and using that instead?

Any advice will be much appreciated!

Answer 1

[Rory Stark]

DiffBind can work with many peak formats, not just bed files as happen to be used in the tutorial. Supported formats are documented on the help pages for ?dba (and ?dba.peakset).

In this case, with ATAC peaks, you can either use the .narrowPeak files and set the PeakCaller values in the sample sheet to "narrow", or use the .peaks.xls files and set the PeakCaller values to macs.

[a_bis]

Thank you, that's very helpful to know!