I am a rookie of processing ChIP-seq data, I get a dataset which is about neuroblastoma. To get the effect of N-myc to histone modification, we knockdown N-myc gene in neuroblastoma cell line, untreated neuroblastoma cell line as control.
About H3K4me3/H3K27me3/H3K36me3/H3K9ac initialfiles. I have run MACS2 calling peak with default settings,I got the peak information in files of .bed、.xls、.narrowPeak.
Next,I think i am going to get the position，maybe promoter information，downstream genes. However，I don't know how to do exactly, can someone help？
It would be more nice if you tell me the software to be used.
Thank you very much!