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I want to calculate density of intra-TAD interactions and inter-TAD interactions for each of the TADs defined by HiCExplorer. Is there any way to do this using HiCExplorer? (Or do I need to calculate …
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```
In [1]: from hicmatrix import HiCMatrix
INFO:numexpr.utils:NumExpr defaulting to 4 threads.
In [2]: cut_intervals = [('a', 0, 10, 1), ('a', 10, 20, 1), ('b', 0, 10, 1), ('c', 0, 10, 1)]
In…
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When I try to build :
```
build_wheel.sh --python 2.7 --package HiCAssembler --version 1.1.1
```
with `config/HiCAssembler-1.1.1.sh` having this content:
```
PATCHES="HiCAssembler-1.1.1.patch…
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Hello,
Thanks so much for the great tool. I'm new to hicexplorer (and bioinformatics, in general) and I had a quick question about normalization and correction.
I've been reading through the docs…
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Hi,
I am very interested in using your tool for pileup analysis.
I was trying to figure out whether is possible to do Local pileups in a strand aware manner.
In particular I am trying to get the …
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// edit: Moved this question to its own new issue. @GregZs Please do not write in old issues, especially if they are already a year closed. Thanks.
Hi,
I am using hicexplorer 3.6 and I am trying t…
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Hi @joachimwolff
this is more of a question/check: in `hicCorrectMatrix correct`, I'd like to make sure the trans reads are ignored. It seems I can do this by setting `--transCutoff 1`. Did I get…
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Hi HiCExplorer team,
Using HiCExplorer, is there a way to plot all of the chromosomes in a given genome while excluding all intra-chromosomal (cis) contacts? That is, show only inter-chromosomal …
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Hi @joachimwolff
I am sorry for the naive question but I can't see what I am missing here.
I used to count the number of cis interactions using simple commands like (here the in.h5 is a plain …
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Hey, I am always getting this error but don't know what does it mean. I processed the hic from juicerbox with a .hic file as the output. I tried to convert .hic to cool file with specific resolution. …