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ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
MIT License
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Compatible with NChIP? #222

Open YogiOnBioinformatics opened 3 years ago

YogiOnBioinformatics commented 3 years ago

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 commented 3 years ago

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

YogiOnBioinformatics commented 3 years ago

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