Hi,
I am currently answering reviewers' comments on our paper https://www.biorxiv.org/content/10.1101/2021.02.16.431334v3.
In this study we used chromVAR to score the enrichment of transposable element subfamilies (instead of motifs) in bulk ATAC-seq data. To answer one of the reviewers' comments I need to assess and provide the number of elements overlapping accessible chromatin in my samples and those overlapping the background files. Is there a way to save the background files as bedfiles or to convert the indexes obtained using getBackgroundPeaks to actual genomic locations?
Many thanks in advance!
Giacomo