HiCExplorer
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deeptools
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
When hicNormalize normalizes cool, it seems use weight in cool for balance first, which results in most of the bin values becoming 0 when using the '-sz 1.0 --normalize smallest'...
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I run the hicBuildMatrix(I use a subset) : hicBuildMatrix --samFiles subset_R1.bam subset_R2.bam --binSize 20000 --restrictionSequence GATC --danglingSequence GATC --restrictionCutFile cut_sites.bed --outBam subset.bam --outFileName ./subset_20kb.h5 --QCfolder ./subset_20kb_QC --threads 8 --inputBufferSize 400000...
Hi, Joachim, I have used 'conda create --name hicexplorer36 hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge' many times and it works fine, but today when I use it again, it is...
Hi All！ When i use hicFindTADs, the following error: multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/public1/home/ligch/miniconda3/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/public1/home/ligch/miniconda3/lib/python3.9/multiprocessing/pool.py", line...
Hello, I'm having issues with `hicDifferentialTAD` for relatively large bin sizes. Domains are called with `hicFindTADs` without any problems. Sometimes it works, sometimes it doesn't. Seems to break for specific...
Hello, I was using HicPlotDistVSCount and got the following error : ``` Command executed: hicPlotDistVsCounts --matrices HIC_ES_4.250000_balanced.cool --plotFile HIC_ES_4_distcount.png --outFileData HIC_ES_4_distcount.txt Command exit status: 1 Command output: (empty) Command error:...
Hi, I want to draw heatmap as below. The heatmap was showing two methods (one is Hi-C ,another is TAC-C) in one picture.  How to make it ? I...
Hi there Thanks for the tools, work really well so far. Just one point that caused quite some confusion. The manual for the normalization step says: --setToZeroThreshold "It is recommended...
Hi, I am trying to install hicexplorer>=3.5 to use hicdetectloops function. Instructions work for mac but not for the Red Hat Enterprise Linux release 8.3 (Ootpa) ) where I anyway...
