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). 

 


You can use MACS, but it is not the best tool for identifying open chromatin regions.  I would recommend using Fseq:  http://fureylab.web.unc.edu/software/fseq/  It was designed to analyze DNase -seq data, the predecessor of ATAC-seq.  When analyzing data from either experiment, you do not really want to look for overlapping reads the way you do for Chip-seq.  You want to look for regions with a high density of cut sights or insertion sights, and Fseq is designed to highlight those.