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**Welcome to the HiCExplorer GitHub repository! Before opening the issue please check
that the following requirements are met :**
- [x] Search whether this issue (or a similar issue) has been sol…
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I am currently trying to figure out why the insulation score computed from the cooltools `_find_insulation_boundaries_dense` looks so odd compared to published data. Sifting through the code I discove…
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**Welcome to the HiCExplorer GitHub repository! Before opening the issue please check
that the following requirements are met :**
- [x] Search whether this issue (or a similar issue) has been sol…
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That I don't forget it for the next bug fix release:
hicInfo sum of contacts: Either the sum or ((sum - digonal)/2 ) + diagonal. But not sum /2.
Related issue: https://github.com/deeptools/HiCExp…
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Hello,
I am running hicDifferentialTAD using this command:
hicDifferentialTAD -tm cools/NlaIII_run01_UCSC_hg38.matrix.cool -cm cools/NlaIII_run03_UCSC_hg38.matrix.cool \
-td run_01/TADs_run01_d…
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Hi @joachimwolff
Using the lastest 3.6 version, I tried to change my WF (in galaxy) to now output `.cool` instead of `.h5` files (at the hicBuildMatrix step); reasoning this will save space and be h…
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hi,
I've met a problem when using `hicPCA 3.4/3.5/3.6` to create pca1.bw and pca2.bw file, the program will **suddenly** exhausting system resources and then be killed. There's no any output. But i…
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Dear all,
In my mind, the following will be a common question when doing PCA analysis.
I resolved the following problem before (https://github.com/deeptools/HiCExplorer/issues/707, mainly because …
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Hi, I run hicPCA with following command :
hicPCA -m hic_corrected.h5 --outputFileName pca1.bw pca2.bw --format bigwig --pearsonMatrix pearson.h5 --method dist_norm --extraTrack NN1138-2.100k.bins.g…
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Dear,
I am using galaxy and therefore the version 3.4.3 of hicexplorer. My problem would be solved with the hicexplorer 3.6 but all my workflows are in Galaxy so I am stuck. Here is the problem, may…