I am new to analysing ATAC-seq data. 

As mentioned on https://www.biostars.org/p/209592/, there seem to be two ways to use MACS to analyse ATAC-seq data. 

1. Utilising the --shift -100 --extsize 200 command 
This, I believe, is to find where the cutting sites are. 

2. Utilising the --shift 37 --extsize 73 command 
This is to find the nucleosomes since the DNA is wrapped around nucleosomes is circa 147bp. 

I specifically want to document regions of open chromatin, particularly enhancer regions. 

I have read in the literature that open chromatin regions will give reads <100bp.  If this is correct, do I have to filter my bam file to look at only this length. 

Surely if I map all of the my data, not filtering for read size I will end up with genome-wide ATAC-coverage? Looking at my bam file following mapping to the genome, my read sizes  range from 50bp-450bp (with a peak at around 70bp). 

 


All these macs2 options that people use, combining shift and extsizes in my experience do not make a notable difference. As spacemorrissey mentioned, unlike ChIP-seq (with typical short single-end reads) you want to scan ATAC-seq data for cutting sites within the accessable chromatin. I always use `macs2 callpeak -g hs --nomodel -f BAMPE`, which skips the macs-typical shifting model and piles up the entire paired-end fragment size.
For reliable enhancer calling, ATAC-seq is the wrong assay anyway, because even though active enhancers are accessible, by far not every accessible region is an enhancer (promoters, silencers, insulators etc...). What exactly is the question you are working on?