Dear all, we are planning to do an ATAC-Seq experiment in human cell lines and we must correct for batches from different time-points. Therefore, we want to use spike-in normalization as described in the DiffBind vignette. For reasons of practicability, we would prefer drosophila chromatin over drosophila cells as spike-in material (we are aware that won't normalize for the cell lysis process). However, we were wondering if it also possible to use plain drosophila DNA instead of chromatin within the tagmentation step. From this, we would expect fragments evenly distributed over the drosophila genome (because all DNA is accessible), which would then be used as spike-in reads in DiffBind to normalize the human ATAC-Seq data. Does this make sense, or do we need spike-in data with reads distributed in peaks and background as obtained with chromatin spike-ins? Any shared experience with spike-in normalization in ATAC-Seq is appreciated. Thank you!
