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elsiklab / gccontent

A JBrowse plugin for plotting GC content and GC skew
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Ambiguous bases are displaying as AT #5

Closed childers closed 7 years ago

childers commented 7 years ago

Runs of N's are counted as 0, and look like runs of A/T. I really like this plugin, as it would save us from manually building GC (and gap) bigwigs.

Below the image includes a bigwig GC Content track, in addition to the GCContent track made using the plugin. A BigWig track showing sequence gaps shown as runs of N is the bottom track.

screen shot 2017-07-06 at 4 26 49 pm
cmdcolin commented 7 years ago

A possible fix for this also on master now, feel free to give it a try

cmdcolin commented 7 years ago

Was this resolved? I think now there is no gccontent data is drawn inside gaps

childers commented 7 years ago

It looks like it is working great now. Thank you! screen shot 2017-08-03 at 4 07 03 pm

cmdcolin commented 7 years ago

Super. I also just added to the latest master a maxZoom parameter for the density track (it already existed on the xy track) so it will display "Zoom in to see GC content" at over a ~1.5MB zoom level (adjustable using the config parameter maxZoom, but if you are calculating over that big regions like this it can slow down browser). Feel free to test out

childers commented 7 years ago

It does slow things down a fair bit on really large views. so the max size cap is helpful.