MACS output files: NAME_peaks.bed

[sergi vas]

Hi,

I am quite new in the use of MACS2, but I've read it is a very useful tool to call the peaks from a Chip-Seq experiment. I am currently working with histone modifications data, and I use the following command to call the peaks:

macs2 callpeak -t file.bed -c input.bed -f BED --nomodel -g hs -n example -B -q 0.01

As you say in the MACS2 user manual, after performing the analysis, many output files should be created. Actually, I obtain many output files, but the NAME_peaks.bed file is not generated. So, do you know why this file is not created? Is there anything wrong with my code? Should I include any parameter to specify the creation of the NAME_peaks.bed file?

My output files are: NAME_peaks.narrowPeak, NAME_peaks.xls, NAME_summits.bed.

Thanks in advice,

Sergi

[Tao Liu]

Hi Sergi,

NAME_peaks.bed is replaced by NAME_peaks.narrowPeak for narrow factor ChIP-seq. NarrowPeak format is a extension of BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format12

Also, to analyze histone modification data, try the 'broad' mode, like:

macs2 callpeak -t file.bed -c input.bed -f BED --broad -g hs -n example -B

It will use a looser cutoff to call a broader region. The output will be in broadPeak format: http://genome.ucsc.edu/FAQ/FAQformat.html#format13

Best,
Tao