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 macs2 command) 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?