Question about output options in runChicago.R

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Thanks for the very nice tool and its precise description in the vignette.

I was wondering if it was possible to use runChicago.R on my data and still be able to perform the downstream QC analyses that you propose, such as <<Visualising interactions>> or <<Peak enrichment for features>>.

Are there any particular runChicago.R output options I should use to be able to do that? and in this case how do I read the output files in R before doing the QC?

Sorry if this is obvious.

Best regards, Sarah Djebali

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