Open chromatin region : nucleosome , mono-nucleosome , di-nucleosome

Question

I m following this tutorial for my ATAC seq analysis. Here in of the section they show profile of open chromatin region plots.

**Plotting insert sizes with Greenleaf open, mono- and di-nucleosome profiles
This looks very similar to the image from the Greenleaf paper.

We can now annotate our nucleosome free (< 100bp), mono-nucleosome (180bp-247bp) and di-nucleosome (315-437) as in the Greenleaf study.**

Now Since i have done the differential accessibility analysis. So from that information how do i find out region which are "nucleosome free (< 100bp), mono-nucleosome (180bp-247bp) and di-nucleosome (315-437) ".

My objective

• I would like to see this "nucleosome free (< 100bp), mono-nucleosome (180bp-247bp) and di-nucleosome (315-437) " from my differential accessible region which was done from readcount and then I ran deseq2.
• My goal is not to plot the way they have done rather find those regions mentioned above and see it between different conditions.

Now based on the tutorial of that section where they do for each bam file.

Do i need to run the analysis on each bam file or each condition or Can I find out the above from my deseq2 analysis which has regions and those regions I have annotated it .

Answer 1

It's impossible to find nucleosome free and such regions without a BAM file. Your only options are:

1. Filter the BAM files to contain only the size-range of interest and rerun the counting and statistics.
2. Find or write a counting program that can track fragment sizes.

BTW, those size ranges could use some adjustments, you're throwing away all fragments between 100 and 180 bases using their ranges.