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Chr.X data do not visualize on Macaca fascicularis 5.0 genome in IGV 2.17.* and 2.18.* #1609

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miwi610 opened this issue Oct 31, 2024 · 0 comments

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miwi610 commented Oct 31, 2024

In both Bedgraph and bigwig, values on chromosome X do not show up in genome-wide or local view in Macaca fascicularis 5.0, which is occuring since IGV 2.17 and later, including current newest IGV 2.18.4.
After checking .genome file of macaca fascicularis 5.0 and 6.0 and rheMac8, I found,

  1. Only 5.0 genome in .genome is labeled without "chr", just "1 2 3 ... X", while .genome in others are labelled as chr1, chr2,,,chrX.
  2. My bedgraph was labelled as "chrX" at first column, therefore I removed "chr" from my bedgraph, just "X", then the data showed up again.
  3. This problem started to appear after 2.17, data with "chrX" was finely visualized in 5.0 genome in IGV 2.16 and before ( I just checked IGV 2.16.2 and it was fine with "chrX" labelled datafile).
    Is it possible to re-set to allow "chrX" in the genome reference with just "X" labelled?
    screenshot1
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