Issues

• FATAL ERROR ML150008291L1C001R00101473806 ML150008291L1C001R00101473960 Be sure that the sam files have the same read order If using Bowtie2 or Hisat2 add the --reorder option

  deeptools/HiCExplorer#960 · Filter by author ZED-rookie opened on Mar 18, 2026
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• hicCorrelate - Can the size of the output image/svg/pdf be adjusted to clearly display the sample names and their corresponding information?

  deeptools/HiCExplorer#959 · Filter by author nooong opened on Mar 2, 2026

• Understanding hicDifferentialTAD output & directionality

  deeptools/HiCExplorer#958 · Filter by author imacarth opened on Feb 5, 2026

• question about buildMatrixMethods.py

  deeptools/HiCExplorer#957 · Filter by author jrw510 opened on Feb 2, 2026

• High align rate but Low reported pairs

  deeptools/HiCExplorer#956 · Filter by author hcph opened on Jan 7, 2026
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• UnboundLocalError: local variable 'out_bam_file' referenced before assignment

  deeptools/HiCExplorer#954 · Filter by author NJU-Bio-Info opened on Nov 26, 2025

• Unequal number of contacts after hicNormalize --normalize smallest

  deeptools/HiCExplorer#953 · Filter by author Ma-Mes opened on Nov 20, 2025
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• hicConvertFormat shall use "HDF5::MCOOL" rather than "HDF5::Cooler" for mcool hdf attribute format

  deeptools/HiCExplorer#952 · Filter by author Fan-iX opened on Nov 14, 2025

• Is the bias(weight) obtained for each bin by the kr method of hicCorrectMatrix a division bias(weight)?

  deeptools/HiCExplorer#951 · Filter by author oganesson76 opened on Sep 25, 2025

• Range of balance correction

  deeptools/HiCExplorer#950 · Filter by author oganesson76 opened on Sep 11, 2025

• Does it support no enzyme cleavage site ?

  deeptools/HiCExplorer#949 · Filter by author normal-154 opened on Sep 8, 2025
  4

• Persistent low-coverage “blue stripes” in Hi-C contact maps (dm6)

  deeptools/HiCExplorer#948 · Filter by author Cathmyt opened on Aug 13, 2025

• Issues with using hicTransform

  deeptools/HiCExplorer#945 · Filter by author HengkuanLi opened on Jul 14, 2025

• Unexpected change in GInteractions row-count after hicNormalize / hicCorrectMatrix, and --load_raw_values flag not giving raw counts in normalized/corrected matrix

  deeptools/HiCExplorer#944 · Filter by author fatimanawmi opened on Jul 9, 2025

• HicNormalize or hicCorrectMatrix

  deeptools/HiCExplorer#943 · Filter by author DakeshiKitano opened on Jun 28, 2025

• Tips for running on a haplotype-resolved reference genome

  deeptools/HiCExplorer#942 · Filter by author marija-kra opened on Jun 25, 2025
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• hicPCA: The A/B compartments of the X chromosome is not properly recognized

  deeptools/HiCExplorer#941 · Filter by author lscnsdad opened on Jun 21, 2025

• TADfind

  deeptools/HiCExplorer#940 · Filter by author mandexue opened on Jun 19, 2025
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• Using Pore-C with HiCExplorer?

  deeptools/HiCExplorer#937 · Filter by author Grisaru137 opened on Apr 22, 2025
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• hicCorrelate: can we retrieve the correlation matrix?

  deeptools/HiCExplorer#936 · Filter by author JosedelasHeras opened on Mar 31, 2025
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• hicAdjustMatrix -- keep whole genomes -- gives list index out of range error

  deeptools/HiCExplorer#934 · Filter by author YanisChrys opened on Mar 24, 2025
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• hicFindRestSites: Restriction site inside another restriction site not written.

  deeptools/HiCExplorer#933 · Filter by author g-pacheco opened on Mar 17, 2025
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• loop compair

  deeptools/HiCExplorer#932 · Filter by author shuairun opened on Mar 17, 2025
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• hicPlotMatrix for translocations/CNVs

  deeptools/HiCExplorer#931 · Filter by author BERICP01 opened on Mar 16, 2025
  2

• UnboundLocalError: local variable 'img' referenced before assignment

  deeptools/HiCExplorer#930 · Filter by author davidecarnevali opened on Mar 13, 2025
  1