ATAC-seq fragment length distribution wrong but data makes sense!

Question

[halffedelf]

Hi fellow biologists, the fragment length distribution of my ATAC-seq data has no peak beyond ~100bp. So basically no peak near nucleosomes. However, the downstream analyses of the data make perfect sense (right motifs show up, right genes nearby etc after differential accessibility analysis).

How do I explain this? How big a deal is the fragment distribution in terms of QC of the data? All other QC factors are good (no of reads, base calling quality, GC content, % mapped reads etc).

[ATpoint]

How big a deal is the fragment distribution in terms of QC of the data?

I'd say the most important one together with the number of peaks and the FRiPs. Can you show a plot for this? It is surprising that downstream makes perfect sense yet the fragment distribution is odd.

All other QC factors are good (no of reads, base calling quality, GC content, % mapped reads etc).

I am afraid that none of this indicates the quality of the ATAC-seq library, this is all just whether the sequencing worked or not.

Can you show a screenshot from a genome browser? Is this human data? Did you see the nucleosomal ladder during library QC on the bioanalyzer?