Comments (2)
Thank you very much for your reply, which solved my question very well!
from chromosight.
Hello,
The default kernels is robust to changes in resolution (i.e. works very well with 10kb matrices), so you don't need to resize it.
We provide a --win-size
option, in case you want to try adjusting kernel size. e.g. the "loops" kernel has a size of 17x17 by default, to 2x larger you would give --win-size 35
(it has to be an odd number). But having such a large kernel just gives worse results usually.
These heatmaps are the actual kernels used for detection. You can edit the kernel files generated by generate-config
however you like to reflect the patterns you are looking for, you could even generate the heatmap with custom scripts and save it into the file. The --click
option just provides an automatic way to do it and is indeed very memory intensive, there is currently no solution to that.
from chromosight.
Related Issues (20)
- How to compare loops of Hi-C from different conditions like DEG in RNA-Seq? HOT 4
- Chromosight for single-cell Hi-C HOT 8
- Point and click mode HOT 8
- Different number of patterns for the same Hi-C matrix HOT 3
- How to evaluate the detected loops? HOT 4
- Different number of loops on GM12878 Hi-C map HOT 2
- chromosight detects hairpin, the numer is too large HOT 1
- Can chromosight detect loops based on restriction fragments level (1f, 2f, etc) HI-C matrix. HOT 2
- Bus error in chromosight quantify HOT 2
- How does Chromosight compute the Pearson correlation ? HOT 2
- Is there a way to use multiresolution .mcool files directly? HOT 1
- Where do these kernels come from? HOT 5
- Loop score calculation HOT 4
- Pattern = TAD? HOT 1
- Recommend parameters of borders detect HOT 1
- Tuning the parameters (perc-zero, perc-undetected, pearson) for a relatively small dataset HOT 2
- HicMatrix generated cool file not supported - possible solution HOT 6
- Handle variable bin size
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from chromosight.