Joachim Wolff
Joachim Wolff
Hi Kevin, Reduce your resolution as I said to 10 kb or better 25kb. Call on 25kb and 10kb resolution TADs, do NOT use a 1kb or a 5kb. What...
Dear Pietro, translocations is actually a topic I wanted to start working on later this year. Right now, I am sorry that it will not work. Maybe I can add...
@pavanvidem I am a bit surprised to see a 3.7.2 version of HiCExplorer be available. I do not know if any changes concerning the 3.7 version which are required in...
Thanks for the suggestion, I will consider it for our next release.
Hi, That should not happen. Did you use a chromosome size file for creating the matrices?
You can use KR normalization or ICE and apply this with hicCorrectMatrix. If you have a cool matrix from somewhere else, we apply by default whatever is written in the...
We scale back to the original value range because we have count values and it is nonsense in our opinion to have therefore values between 0 and 1. bxhu ***@***.***>...
ICE is the algorithm as described by Imkaev 2012: https://pmc.ncbi.nlm.nih.gov/articles/PMC3816492/ You have the assumption that every region should interact with all other regions in sum by the same amount. That...
Cooler does not scale the values back. The KR correction transforms all values to the 0-1 range. In HiCExplorer we expect the data to be in the original data range....
Why do you think it works only for h5?! It works for the cool-format of course too. Whole HiCExplorer supports for ALL its tools the cool format natively. Normalization is...