What method was used in the paper to convert the predictions into valid pairs?

[rebeccaronai]

I saw in the paper it states that "we converted the predicted matrix back to valid pairs by merging predictions to chromosomes and counting the discretized intensity value." I also saw that someone raised the issue and it was closed stating it takes a lot of effort. I am wondering if you can specify what method was used in the paper so that it can be replicated by others and FitHiC can be used for loop calling?

[tanjimin]

Hi @rebeccaronai , I'll describe the main idea here:

1. After predicting with C.Origami, you will have a 2mb by 2mb or 256 by 256 bin matrix.
2. For each pixel at location $i$, $j$ in the 256x256 grid, you can perform exponential transformation ((exp x) - 1) to convert log1p reads to reads $n$.
3. The reads $n$ you get will be the predicted number of Hi-C valid pairs between location $i$ and $j$. Then you can convert $I$ and $j$ to actual genomic regions and add $n$ lines of $i$ $j$ interaction. You can do this for all regions across the genome then you will end up with a predicted valid pairs file.
4. You can then run FitHiC on this predicted valid pairs file.