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.
I have added
--nomodel --extsize 197;
--nomodel --extsize 147and
--nomodel --extsize 202(separately to
macs2command) and got the results without any warning? which one is more correct?
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?
which kind of peak (narrow/broad) is proper for H3k27ac, H3k4me1, H3k4me3,H3k27me3 study?
if there is no control group for using as background, can I use default parameters?
Thanks for any suggestion, in advance!