Minimum spacing between viewpoints?

[Noboru Sakabe]

Hi, this is not an issue but maybe other people will find this question useful. Will ChICAGO have a problem with a dataset whose viewpoints/anchors are very close from each other? Let's say there are 100 viewpoints/anchors and they are all within 10 kb. Many of the probes would be shared by the viewpoints. What would happen in this case? I imagine the signal will be the same across several viewpoints. One reason for overcrowding is to increase the chance of capturing fragments but I wonder if this will cause problems in the analysis. Thank you.

[Jonathan Cairns]

Hi,

I would expect CHiCAGO to run fine in that situation. With 100 baits in a 10kb region, CHiCAGO should still have enough bait-to-non-bait information to calculate the distance decay curve.

In contrast, however, a 1mb contiguous baited region would be unlikely to work, because most of the short-range reads are bait-to-bait. In that situation, I think it's usually better to take only the bait-to-bait read pairs and run a Hi-C analysis).

Thanks,

Jonathan

[Noboru Sakabe]

Thank you. I'll come back for help if I run into problems!