java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.

Google Groups | Unknown author | 12 months ago
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  1. 0

    input files with no restriction fragments information

    Google Groups | 12 months ago | Unknown author
    java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.
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    The .hic files are too small, inter.txt and inter_30.txt claim I only have inter-chromsomal reads

    Google Groups | 5 months ago | Ittai Eres
    java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.
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    Problem in juicebox48g (Java program)

    Google Groups | 8 months ago | Zhong Wang
    java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.
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  5. 0

    input needed to create .hic file using pre command

    Google Groups | 8 months ago | rdali
    java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.
  6. 0

    No reads in Hi-C contact map

    Google Groups | 2 months ago | Unknown author
    java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.

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    Root Cause Analysis

    1. java.lang.RuntimeException

      No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.

      at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.mergeAndWriteBlocks()
    2. juicebox.tools.utils
      Preprocessor.preprocess
      1. juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1387)
      2. juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1158)
      3. juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:572)
      4. juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:303)
      5. juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:213)
      5 frames
    3. juicebox.tools.clt
      PreProcessing.run
      1. juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:94)
      1 frame
    4. juicebox.tools
      HiCTools.main
      1. juicebox.tools.HiCTools.main(HiCTools.java:78)
      1 frame