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Dark reads in pile-up track

asked 2021-04-12 08:01:18 -0700

Lucas Michel Todo gravatar image

When displaying some tracks in the browser, in the wide-zoom view, some reads in the pile-up track appear dark (almost black). The color of the pile-up track quickly shifts from the ususal green to black in some areas and I can't identify a reason for it, since the underlaying reads don't seem to have consistent differences in mapping quality or amount of missmatches.

Thanks very much in advance!

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answered 2021-04-21 06:37:26 -0700

Hi there,

I might need a screenshot to provide a more concrete answer.

Depending on the zoom level, the height of the reads may start to become so small that the color appears darker. You can adjust the zoom in the vertical direction directly by togging the little zoom mode button in the top-right of the plot that has a letter like "A", "F", "H" or "M" on it.

When the view zooms out to show the precomputed coverage, the Pile-Up plot will show per-base mismatch data as black so it is easy to identify areas of mutation.

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Asked: 2021-04-12 08:01:18 -0700

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Last updated: Apr 21 '21