Entering edit mode
10 months ago
onca • 0
Is there anyway of selecting a list of reads in IGV? I would like to highlight a group of reads based on their ids or coordinates. I have duplicates on my RNA-Seq that I would like to visualize in IGV.
In fact, I have already run Picard MarkDuplicates which indicates the duplicates through sam/bam flag field. But it can also add a duplicate type (DT) tag:
Do you think if I re-run Picard MarkDuplicates with this option I will be able to highlight the duplicates in IGV (through "Color alignments by > tag > DT")?
Just an update: I was indeed able to visualize the duplicates in IGV by "Color alignments by > tag > DT".
IGV image with duplicates highlighted in red:
DT tag in bam file (only for duplicates):