Ask Your Question
0

Dark reads in pile-up track

asked 2021-04-12 08:01:18 -0600

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!

edit retag flag offensive close merge delete

1 answer

Sort by ยป oldest newest most voted
0

answered 2021-04-21 06:37:26 -0600

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.

edit flag offensive delete link more
Login/Signup to Answer

Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.

Question Tools

Follow
1 follower

Stats

Asked: 2021-04-12 08:01:18 -0600

Seen: 30 times

Last updated: Apr 21