Percentage of Adenines taken into account for nucleosome calling?

[AnnaE-F]

Hello,
Thank you for developing the tool!
We were wondering if you take into account, when calling nucleosomes, the percentage of Adenines in a region. In particular, if there is a region with no Adenines, there will be 0% methylation, so will the tool interpret it as a fully inaccessible region and predict a nucleosome?
Best

[mrvollger]

We do not account for this right now. Since the false positive rate of m6A is low and ~100bp of only GC bases is rare we think it's a very infrequent issue. But we are hoping to revisit the nucleosome caller in the future to account for things like this.

Cheers,
Mitchell

[AnnaE-F]

Thank you for your answer! Best, Anna