I am new to analysing ATAC-seq data.
As mentioned on ATAC-seq peak calling with MACS, there seem to be two ways to use MACS to analyse ATAC-seq data.
Utilising the --shift -100 --extsize 200 command This, I believe, is to find where the cutting sites are.
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).