I am trying to call peaks in ATAC-seq data. Not surprisingly, MACS is a popular option. According to the [MACS documentation][1]:

> 1. To find enriched cutting sites such as some DNAse-Seq datasets. In this case, all 5' ends of sequenced reads should be extended in both
> direction to smooth the pileup signals. If the wanted smoothing window
> is 200bps, then use '--nomodel --shift -100 --extsize 200'.
> 
> 2. For certain nucleosome-seq data, we need to pileup the centers of nucleosomes using a half-nucleosome size for wavelet analysis (e.g.
> NPS algorithm). Since the DNA wrapped on nucleosome is about 147bps,
> this option can be used: '--nomodel --shift 37 --extsize 73'.

Based on a brief literature review, people use both `--shift -100 --extsize 200` and `--shift 37 --extsize 73` for ATAC-seq. Is one option more appropriate? Are there maybe different sub-types of ATAC-seq where one is better than the other?


  [1]: https://github.com/taoliu/MACS
I got another alternative from the MACS developer:

> If you followed original protocol for ATAC-Seq, you should get
> Paired-End reads. If so, I would suggest you just use "--format BAMPE"
> to let MACS2 pileup the whole fragments in general. But if you want to
> focus on looking for where the 'cutting sites' are, then '--nomodel
> --shift -100 --extsize 200' should work.

And then more recently:

> Why do so many papers use --shift -100 --extsize 200 for MACS2 rather
> than -f BAMPE if this is not recommended for paired-end data?
> 
> --shift -100 --extsize 200 will amplify the 'cutting sites' enrichment from ATAC-seq data. So in the end, the 'peak' is where Tn5 transposase
> likes to attack. The fact is that, although many information such as
> the insertion length and the other mate alignment is ignored, such
> result is still usable. Especially when the short fragment population
> is extremely dominant, the final output won't be off much.

Source: https://github.com/taoliu/MACS/issues/145
