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 !!