Read alignment track with split parts joined by thinner lines#

Create a SplicedReadTrack to show the alignment in a BAM file, the spliced parts will be rendered as thinner lines.

chr22
[<Axes: title={'center': 'chr22'}, ylabel='RNA-seq'>]

from pygv.viewer import GenomeViewer
from pygv.tracks.bam_track import SplicedReadTrack
gv = GenomeViewer()
track = SplicedReadTrack(
    "../examples/data/s03.chr22.bam",
    name="RNA-seq")
track.sampling_ratio = 0.3
track.color_reads_by = "first of pair strand"
track.line_width = 0.3
gv.add_track(track)
gv.plot("chr22", 40349785, 40353365)

Total running time of the script: (0 minutes 0.181 seconds)

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