search

ay-lab / mustache

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
MIT License
64 stars 11 forks source link

Calculation of distance limit? #35

Closed fboellmann closed 3 years ago

fboellmann commented 3 years ago

Since I specified -d 250000000, I can see that the actual max distance metric is 2000 fold higher than my bin size (6Mb, 10Mb, 20Mb for 3k, 5k 10k bin size). Is that hard coded or does that take available RAM into consideration? I am evaluating mustache for shorter loops anyways, so no biggie, just curious.

ay-lab commented 3 years ago

Hi, yes it is hardcoded. RAM is one of the reasons. The main reason is that detecting more distant loops comes with the price of missing some short distance loops. You can hardcode the distance you want by uncommenting and changing the line#1048 (#distFilter = 4000000).