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https://github.com/maxplanck-ie/snakepipes/blob/55950653f15d14cad356dd636da28247681e1027/snakePipes/shared/rules/hicexplorer.snakefile#L67
`-rs DpnII.bed --restrictionSequence GATC --danglingSeque…
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PC1 and PC2 tracks in the TADs plot look different from the PC1 and PC2 tracks in the TADs plot of the HiCExplorer tutorial figure. However, my PC plots underneath the pearson matrix are the same as t…
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Hi,
If multiple restriction enzymes are used, blunt and sticky. What is the correct way to use the function hicBuildMatrix?
I used findRestSite function to find restirction site for all enzymes, in…
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Not a bug exactly, but I am using fastp instead of afterqc and notice it is not supported, even though it is supposed to be and implementation of the same thing (not sure if/how the output file has ch…
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Hi,
I used hicexplore (v2.2.1.1) to build and correct matrix,
```
hicCorrectMatrix correct \
--chromosomes chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr1…
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I was debugging hicexplorer execution using the current bioconda image, and there the interpreter quits with exit code 1.
That seems less than ideal:
```
Python 3.6.7 | packaged by conda-forge | (d…
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I installed hicexplorer using conda:
```
conda create --name hicexplorer3.4.1 hicexplorer=3.4.1 python=3.6 -c bioconda -c conda-forge
conda activate hicexplorer3.4.1
```
Running hicPCA and hicTra…
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I see that this issue may be relevant https://github.com/ewels/MultiQC/issues/844
**Description of bug:**
Multiqc cannot recognize output from rseqc/geneBody_coverage2.py
**MultiQC Error log:…
whtns updated
4 years ago
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When I try to run hicDetectLoops on a cooler I get the following error, which repeats until I cancel the command:
Process Process-1:
Traceback (most recent call last):
File "/usr/lib/python3.6/…
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pytables >= 3.5 was needed when installed this HiCExplorer ,but I only found 3.2.0, Is there is an >= 3.5 version or not ? can you give me an download URL?