Question: An odd number of differential peaks in MACS2
gravatar for nehoralevi
7 months ago by
nehoralevi0 wrote:


I'm working with ChIP-seq data and using MACS2 version- macs2 I run MACS2 callpeak twice for two different data sets to find the enrichment peaks for each one of them. I got 22,830 peaks at the first and 28,911 peaks at the second, when I use the bdg files for running bdgdiff it find only 6 and 183 differential peaks. why does MACS2 remove so many of the peaks? in which parameters should I focus on? thanks,


bdgdiff macs2 chip-seq • 332 views
ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by nehoralevi0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


First, try using the most current version of all tools - example: MACS2 bdgdiff Differential peak detection based on paired four bedgraph files (Galaxy Version

Next, it may be that the data really do not have much difference, but you can experiment with the different parameters on the tool form. Each is described - I would suggest starting with the scaling (sequencing depth).

Galaxy tutorials:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k
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