HicNormalize or hicCorrectMatrix #943
Description
Dear developers,
Many thanks for you amazing pipeline. I was wondering, what should come first hicNormalize with '--normalize smallest' setting, or hicCorrectMatrix? Or using just one of them is sufficient?
I tried to understand how threshold for ICE matrix correction are selected, but I didn't find a clear guideline of doing that. I even checked paper by Imakaev, for whom you refer to, for using ICE, but that paper does not clearly state the procedure of selecting thresholds based on hicDiagPlots.
Best regards,
Daulet.