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Hi, I run hicPCA, but some of A/B compartment (based on pc1 value positive and negative) is totally flip compare with RNA peak data. Like for gene rich region, it should assign positive value, but res…
mw18f updated
4 years ago
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Hello,
I am working with HiCExplorer. Used conda for the installation, so far, I was able to use the commands: hicConvertFormat, hicPlotMatrix, hicCorrectMatrix, hicFindTADs, hicPlotTADs and hicPCA w…
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Currently it has 81MB of test data, the upload limit for toolshed is 64MB. Is all this data necessary for testing the Galaxy wrapper?
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-rw-r--r-- 1 marten staff 1.2M Oct 17 2018 tad_score.…
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I have attached my .ini file and the output, and the command is here:
hicPlotTADs --tracks dmel_dup1.ini -o dmel_dup1.png --region dmel_muller_A:5500000-6500000 , and the output. The
This was run…
nt365 updated
4 years ago
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Hi,
Thank you for the amazing tool. I am a graduate student learning to use the tool. I am plotting log transformed normalized .h5 matrix using v3.0. I was wondering how the values of two plotting me…
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Hi,
I am wondering if there is a tool for simultaneously converting cool files, or is there anything wrong with my code. I tried to use shell to write a for loop but doesn't work. (This code works fi…
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Hi,
I'd like to use hicBuildMatrix to convert from BAM files to matrix format.
The data is Capture C preprocessed with HiCUP.
I use the dedupped filtered BAM files from HiCUP as input for hicBuildM…
chesi updated
4 years ago
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I installed a software named HiCExplorer ,and pytables >= 3.5 was needed ,but I only found 3.2.0, Is there is an >= 3.5 version or not ? can you give me an download URL?
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Hi @gtrichard @joachimwolff ,
I have observed the similar behavior of hicPCA as described in https://github.com/deeptools/HiCExplorer/issues/346
As suggested, I masked the centromere. Most of th…
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Hi!
For plotPCA function, I have some problems.
I wasn't able to clearly understand this input format of gene track file. In fact, no matter whether I use the bigwig file of gene density or the …