ATACseq: Extract Mono-nucleosome information from di- and tri-nucleosome data

Question

[Deep]

Hi,

My objective is to split di- and tri-nucleosome ATAC-seq data points into mono-nucleosome and then consolidate the total ATAC-seq (mono-, di- and tri-) nucleosome information into one data file representing mono-nucleosome data (if possible in sam format).

I eventually want to generate bigwig files from consolidated mono-nucleosome data and plot nucleosome occupancy / positioning heatmap or line graph using deeptools and want to call consolidated mono-nucleosome peak as well using macs.

In other words, With respect to this information "Dinucleosome reads were split into two reads, and trinucleosome reads were split into three reads." given in the paper Buenrostro et al, 2013 (https://www.nature.com/articles/nmeth.2688#Sec9)

May I request you to advice me on the strategy I should follow to write a custom script to perform the same kind of data processing as mentioned above (instead of using any ATAC-seq package like NucleoATAC etc)?

Thanks, Deep

[ATpoint]

You probably want https://deeptools.readthedocs.io/en/develop/content/tools/alignmentSieve.html

[Deep]

Hi ATpoint, Thanks for your reply. After going through the documentation, I understand that I can extract di-nucleosome and tri-nucleosome data from the total ATAC-seq data. What I could not figure out is, how can I split the di-nucleosome into two mono-nucleosome data points and also tri-nucleosome into three mono-nucleosome data points (preferably in BAM format). I will appreciate your advice. Thanks

[ATpoint]

I never understood that sentence from their paper tbh. In my head NFR is everything below 200bp, mono is alignments with insert size 200-400, di is 400-600 and so on.

[Deep]

Thanks, I appreciate your response.