Should the users be concerned about the problem raised in the new Contradictory Results bioRxiv preprint? about chess HOT 2 OPEN

Hi, and thanks for the question. We are aware of the preprint and are drafting a detailed response to it. With appropriate parameters and thresholds, the CHESS output can be used to identify real differences between Hi-C datasets. We're also in the process of drafting more in-depth guidance on how to choose these parameters and thresholds, which we'll add to the FAQ when it's ready and let you know!

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Hello,
Our preprint is available online now: https://www.biorxiv.org/content/10.1101/2021.10.18.464422v1 We've also updated the CHESS docs and FAQ with some additional guidance on best practices for using CHESS. I hope that clears up any concerns. We'd be happy to answer any follow-up questions you have!

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