Peak detection using MACS

[Ayyappa_kumar]

I have performed peak detection on my sample data which has one treatment sample and once control sample, It has resulted me with four lists: a) NA_Negative peaks, b) NA_Peaks.bed c) NA_peaks.xls d) NA_summits.bed.

I have used the NA_Peaks.bed for motif detection, but am not sure regarding my selection? And also does NA_Negative peaks list represents the peaks obtained from the -ve Strand? Any suggestions will be really helpful !!

[paolo.kunder]

In MACS README file is well explained:

http://liulab.dfci.harvard.edu/MACS/00README.html

NAME_peaks.xls is a tabular file which contains information about called peaks.

NAME_peaks.bed is BED format file which contains the peak locations.

NAME_summits.bed is in BED format, which contains the peak summits locations for every peaks. The 5th column in this file is the summit height of fragment pileup.

NAME_negative_peaks.xls is a tabular file which contains information about negative peaks. Negative peaks are called by swapping the ChIP-seq and control channel.

[Ayyappa_kumar]

Thanks for your reply !!!

So one should use peaks.bed file for motif detection, please let me know if am not wrong.