Hey,

I started playing around with Gviz for visualizing aligned RNAseq reads and
have been pretty impressed, particularly with integrating external
annotation with read-level data. I've been able to get  multi-paneled plots
depicting reads and corresponding coverage in specific regions - I wanted
to

a) confirm that reads from the same fragment are what are connected with
lines (and do not indicate junctions, unlike IGV) and

b) know if it was possible to color reads that contain junctions in a
different color than reads without a junction (e.g. color by the `ngap`
column being greater than 0 when `readGAlignmentPairs` or `readGAlignments`
is used to read in a bam file)

I tried looking online but had a hard time finding anything

Thanks,
Andrew

	[[alternative HTML version deleted]]

