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  • #31
    Hi Jim,

    IGV is a great tool! I use it all the time. I have a question about the “coverage”. I hope to view all the reads mapped to a region, according to IGV, the depth of the reads is about 1000. However, I am not sure whether IGV has displayed all the 1000 reads, since if I use the “expanded” view, the number of the gray bars (I assume each gray bar represents one read) doesn’t seem to be 1000. I tried the change the “Maximum read depth” under “Alignment” of the “Preferences”. However, the number of the gray bars doesn’t seem to increase. I probably missed something on the user’s manual. Thank you very much!

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    • #32
      Hi, IGV downsamples to "max read depth" for display, but counts all reads for the coverage., Changing the "max read depth" value it is the correct way to see more, you didn't miss anything. It should refresh automatically, did it seem to reload after changing the value?

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      • #33
        Hi Jim, thanks! I closed the brower and reload the file, and now I can see all the reads.

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        • #34
          OK, thanks for reporting back. That is a bug, it should have reloaded without having to quit. I'll note it and fix it in an upcoming release.

          Jim

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