# Macs2 peak calling?

I have paired end ChIP-seq data with 101 bp and 2 biological replicates for each one. I have done peak calling with macs2 but I have some questions about it.

I also faced with an warning:

WARNING @ Thu, 07 Jun 2018 17:06:05: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem!
WARNING @ Thu, 07 Jun 2018 17:06:05: #2 You may need to consider one of the other alternative d(s): 197
WARNING @ Thu, 07 Jun 2018 17:06:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing.

1. I have added --nomodel --extsize 197 ; --nomodel --extsize 147 and --nomodel --extsize 202 (separately to macs2 command) and got the results without any warning? Which one is more correct?

2. Are broad peaks extended of narrow peaks? If I apply intersect between them I should expect find 100% overlap between narrow peaks and broad ones?

3. Which kind of peak (narrow/broad) is proper for H3k27ac, H3k4me1, H3k4me3, H3k27me3 study?

4. If there is no control group for using as background, can I use default parameters?

1. Your original command without --nomodel --extsize ... is probably the most accurate. This warning stems from a time when reads were much much shorter and likely never made that much sense to begin with.
2. Broad peak calling in MACS2 basically works by finding a bunch of nearish narrow peaks and merging them. If you have really broad signals then use something like histoneHMM instead.