Rtracklayer export.bedGraph trackLayer color format unable to read by UCSC genome browser
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tanas80 • 0
@tanas80-20056
Last seen 5.6 years ago

I am trying to generate bedGraph track file from GRanges object in R using rtracklayer package. I have found that export.bedGraph() routine uses 'score' meta column of GRanges object and can be supplemented with trackLine argument of class GraphTrackLine as track header. Constructor of new('GraphTrackLine', ...) object requires color argument of type integer (vector). I have provided argument value color=col2rgb("red")[,1] and results output track header formatted as

track name=<name> description=<desc> color="0","255","0"

While IGV is able to open and present the same file, but UCSC Genome Browser 'MyData/Custom Tracks/Add custom track' fails with

Error File 'filename.bedGraph' - line 1 of custom input: variable needs to start with letter ',"255","0"'

Please help me to workaround color property format incompatibility.

software error • 656 views
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Your question is pretty close to undecipherable. Please read the tutorial for posting to this support site, and reformat.

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James, thank you for your interest. I have tried to highlight keys in question. Please be lenient with I'm not a native English speaker.

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