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Using MACS2 for peak calling
Entering edit mode
19 months ago
anais1396 • 20

Hello everyone !!

I am new in dealing with peak calling and I chose macs2 for doing this on ATAC-seq samples.

I performed a mapping with bowtie on my samples (which are 2 replicates) and I selected only the chr6 from my bam files after the mapping (to reduce the file's size). Then I used markduplicate from Picard (with option remove_duplicate=true) to detect and remove duplicate reads from my files. So now I need macs2 to make peak calling but I don't really understand how it works... The documentation about it is not really clear for me...

Can someone explain me how would I choose the good parameters ? the good qvalue ?

I made some tests on my samples and after the peak calling, I used jaccard metric (index of similarity)on my bed files to know if my 2 replicates have peaks in common but they are quite differents...but they are replicates !! So I don't understand this result... I just noticed that the more increase the qvalue in my command line in macs, the more the samples are similar.

Here is my command line in macs2 :

macs2 callpeak -t replicate1.bam -f BAMPE -g 1.8e9 -n macs2_replicate1 -B -q 0.1

(-g 1.8e9 = size of the chr6)

What I'm looking for is to find good parameters in macs2 to calibrate them on my replicates to have 2 files which are similar at the end. Then I could use this parameters on 2 other files of ATAC-seq and compare them to know if they have peaks in commun or not. Is there another way to do this maybe ?

Thank you in advance for your help !!


Entering edit mode
17 months ago
Hussain Ather • 920
National Institutes of Health, Bethesda…

The default parameters generally perform pretty well. You could try running MACS multiple times with various parameters and visualizing the results in IGV or UCSC Genome Browser to determine how the parameters shape the peak-calling behavior.


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