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Hi, I am trying to install HiCExplorer with conda, python 3.8. However when I try to install it, running:
conda install hicexplorer=3.6 -c bioconda -c conda-forge --debug
I get the following err…
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Hi all, I'd like to request clarification on the workflow and arguments for application of Juicer KR correction factors to HiCExplorer hic2cool-converted matrices.
##### Step 1
```
hicConvertForm…
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Hi, I also have a similar issue as my colleague raises the question below. I found that boundary sizes differ (5 to 7% of boundaries) after matrix correction (--correctionMethod ICE). I'm using the 3.…
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Hi,
First, thank you so much for the amazing tool. We recently put a paper on bioarchive, and it couldn't have been possible without this user-friendly tool.
I was wondering if you guys are developi…
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In the "Loop Detection using..." paper, it says that HiCExplorer runs in ~3 minutes. However, when I call hicDetectLoops it takes ~2 hours to run. What is the source of this discrepancy? Am I using it…
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Hi, for some reason HiCExplorer returns zero loops. I am currently running the following code:
hicDetectLoops -m data_800.cool -o 400_loops.bedgraph -tpc 16 --windowSize 10 --peakWidth 6
Where the d…
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Dear,
I am running hicBuildMatrix 3.5.3 on a pretty big BAM pair (4 nextseq high lanes merged => 80G each) using the command line:
```
hicBuildMatrix --samFiles Fwd-Reads.bam Rev-Reads.bam --outF…
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Hi, I have confusion on the output of hicFindTADs.
From the *_tad_score.bm file, I find that the binsize in each row is varying. The hic resolution is 2kb. Why the bin size in each row are not equal…
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Hi. I'm trying to convert a typical `.hic` file to `.h5`. The command:
````
hicConvertFormat -m /full/path/to/aligned/inter_30.hic -o outfile.h5 \
--inputFormat hic --outputFormat…
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Dear,
this is not an issue but I cannot find a way to filter out the inter-chromosomal interactions from a h5/cool matrix.
Actually what I'd like to do is to `hicNormalize` a list of matrices to …