Coloring reads in AlignmentsTrack based on mapq
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@vinicius-henrique-da-silva-6713
Last seen 11 months ago
Brazil

Is it possible to change the fill color of the reads in a track obtained from the AlignmentsTrack() function, library(Gviz) package based on its mapping quality (i.e. mapq)?

I searched for something similar to groupAnnotation from AnnotationTrack() but it seems that such a parameter is not present in for AlignmentsTrack().

I tried the below code but it does not work:

afrom <- 44945200
ato <- 44947200

alTrack <- AlignmentsTrack(
  system.file(package = "Gviz", "extdata", "snps.bam"), isPaired = TRUE, 
groupAnnotation="mapq")
plotTracks(alTrack, chromosome = "chr21", from = afrom, to = ato)

Any idea to get around this?

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