ATACseq fragment/insert length distribution: Peak of Mononucleosome Fragments larger than the NFR peak

Question

[ahnje770]

Hello,

I've noticed that the mononucleosome fragment peak (~200bps) is larger than the nucleosome free fragment peak (~100bps). Since it's usually the other way round I was wondering what people thought about this? is this something of concern?

This data was generated using the OmniATAC protocol using a breast cancer cell line. 75bps pair-end sequencing and reads aligning to the mitochondria were removed.

[ATpoint]

I would not overinterpret these metrics. Just check how the data look on a genome browser, so whether there is clear separation of signal and noise and calculate the FRiP, so the percentrage of reads overlapping callable peaks. That is usually for a good library something > 10%, we often get up to 50% in very good samples. I think if this distribution here indicates something fishy then it will manifest in other QC metrics or somewhere in downstream analysis, and if not then ignore it.

[ahnje770]

Hey Alexander. Thanks so much for clearing that up! FRIP is around 50% for all of them and bigwig peaks look good in IGV. Cheers, Antonio.