Handling 4DN .mcool files

[wangfuzhou110]

Hi,

I noticed that a warning message has recently been attached to many .mcool files in 4D Nucleome Data Portal. For example, click the note here will show the warning message:

WARNING - Due to a bug in the version of cooler (0.8.3) used in the current 4DN standard Hi-C processing pipeline some pixels may occur mulitple times at a single resolution with different counts being reported for each occurence. This duplication does not affect the higlass display of these files, howevver, downstream analyses using this file may encounter issues due to this pixel duplication. The counts from the duplicate pixels can be aggregated to determine the correct count value at that location. If this issue is problematic for your needs you should consider regenerating the matrices from the merged pairs file of the associated dataset using a more recent version of cooler. We are working to update the pipeline but do not yet have a predicted date for when this issue will be resolved.

I wonder if FAN-C is able to handle/solve this duplicate pixel issue naturally? Can we still directly use FAN-C to analyse these potentially problematic data?

Fuzhou