bowtie --cutntag -X 700, ATAC-seq, maxfragment size

[sunta3iouxos]

In you ATAC-seq pipeline the default seting for the --maxFragmentSize is 150. This setting will exclude the mono-di-tri-nucleosomes that provide also a very good overview of the state of chromatin.
In addition, the default settings should be changed to something like 800, or even 1000, considering that nucleosomes in the ATAC-seq should be of sizes 200, 400,600.
Same with the bowtie -X rule set in --cuntag. Because those settings can also be used to call for the ATAC-seq peaks, same enzyme used for both methods.