Compatible with NChIP?

[YogiOnBioinformatics]

Hello @akundaje and @leepc12 ,

I wanted to use this pipeline to analyze ultra-low-input, native ChIP-Seq samples ULI-NChIP looking at histone modifications.
Unlike regular ChIP-Seq, ULI-NChIP uses MNase for digestion (instead of sonication) and avoids cross-linking protein-DNA interactions.

Considering that the histone pipeline would expect the standard histone ChIP-Seq, would there be a problem using this pipeline?

Furthermore, MNase is known to have it's own biases and so I wonder....
Whether the normal ChIP-Seq library complexity QC parameters are still valid to exclude samples?

[YogiOnBioinformatics]

Super sorry but just want to follow up on this. 😄
@akundaje @leepc12

[YogiOnBioinformatics]

I know it's been a while @akundaje and @leepc12 but just wanted to follow up on this!