I have a few questions about ATAC-seq data analysis. My lab is using ATAC-seq to identify accessible regions in the chromatin and check for differential chromatin accessibility between disease and control state as well as checking for TF binding in open chromatin regions (we usually do motif analysis for this). We currently do not size select our data and we do paired end sequencing.
In order to do motif analysis, should we remove fragments that correspond to nucleosomal reads? Since TFs usually bind in nucleosome free regions, it doesn't make sense to me that we keep larger, nucleosomal fragments. However, I have seen many papers that do not do any sort of size selection (experimental or computational) and I am wondering if I am missing something.
Second, is it necessary to do paired end sequencing for ATAC-seq if we do size selection during library prep? I have also noticed that almost everyone does paired end sequencing for ATAC but I'm not sure why this is the case?