Nice to meet you all. I'm new to NGS data analysis. I have received
H3K9me3 ChIP-seq. data, which peak calling was conducted by
MACS2. I've observed that there are different enrichment pattern of the K9 signal (see below). I am concerning that the parameter for peak calling is not appropriate since the broad signal was called as separate small peaks. I know the
--broad argument can be applied when handling broadly distributed histone modification signal, so that the nearby singal can be linked into a broad peak. However, if
--broad is applied, will it affect the calling of those sharp peaks? Thanks.
: https://i.imgur.com/BhUQ8nZ.jpg Relatively sharp peak at promoter
https://i.imgur.com/yJ6VNFt.jpg Broad signal over gene body
: https://i.imgur.com/33eEeln.jpg Sharp peak at intergenic region