macs2 param for H3K27me3 and H3K9me3

Question

[chipseq33]

Hello,

I am running Macs2 to call broad peaks H3K27me3 and H3K9me3 on my chipseq data. I strangely get a very low number of peaks less than 1000. can you tell me what could be the reason? can you share optimal MACS2 param for calling H3K27me3 and H3K9me3? Thanks

[Devon Ryan]

Before playing around with parameters, have you (A) checked how well the signal is enriched (e.g., with plotFingerprint in deepTools) and (B) had a look at the BAM files in IGV?

[ivivek_ngs]

I think also CHANCE can be used to check the quality of the signals enriched and then if there is a drop one can use relaxed parameters for peak finding, as per my experience these are broad profiles so if the broad and broad-cutfoff should be switched on, if you by -q 0.05 and --broad-cutoff 0.1 still you get very low peaks then you can use -p to a higher stringency like reported in macs1.4 as 1e-7 and then filter out top peaks based on log10(pvalue) and farther by fold enrichment scores.