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`SlurmEasy -m 10G -t 12 -l logs 'hicPlotMatrix --matrix matrix_corrected.cool --outFileName matrix_corrected_cool_log1p.png --log1p '`
`INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True
Tr…
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Hello,
I used hicPCA `version 3.5.3` with a gene track (bed6 format)
`hicPCA --matrix "matrix.h5" -o "PC1-flip.bw" "PC2-flip.bw" "PC3-flip.bw" -noe 3 --extraTrack "dmel-all-r6.genes.chrfiltered.b…
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Question. I have a bedpe file containing loop coordinates, and I would like to extract the read count (total|mean|median) for a given matrix file (H5/cool) across each of these regions in the bedpe fi…
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Hello hicexplorer team,
I have a couple of issues with hicexplorer which I’m trying to install with conda. I tried all possible options with conda supporting python 2.7 but then I don’t get tools v…
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Hi, I want to use hicTransform module to analysis the A / B compartments as you described in documentation ,but when I run hicTransform as following command :
hicTransform -m hic_corrected.h5 --ou…
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Hi, I ran your HiC analysis pipeline.
At first, everything is going well. However, after 8 hours, some error messages produced:
"Error in rule build_matrix:
jobid: 5
output: HiC_matrices/k…
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Hi,
very basic question!
is adapter trimming of fastq Hi-C raw reads needed before to use Hi-Explorer mapping parameters? Thanks
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https://gist.github.com/mvdbeek/dfad7627d8dc52104fff24a838484cb1 has the failing tests for the IUC repository (i’ve removed the ones that fail on 20.05 as well, that’s why the numbers don’t add up). W…
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Hi there,
I recently calculated TADs from Hi-C generated in both WT and a KO system. TADs were calculated using hicexplorer's hicFindTADS function and regions with differing TAD structure were iden…
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Hello,
I used hicPCA (version 3.5.3) on Hi-C matrices
` hicPCA --matrix matrix.h5 -o PC1.bw PC2.bw -pm Pearson.h5 `
and then wanted to look at the hicInfo results on the Pearson matrix
` hicIn…