Hi all,
from Integrative Genomics Viewer User Guide (Paired-end alignments - IGV Desktop Application), when an inversion shows up in paired-end reads, there should be both RR reads and LL reads. As shown below.
When I use the orientation of Illumina paired reads to detect inversions, I found a region only have RR reads, see the picture below. I used color alignments by pair orientation, and view mate region in split screen. I don't know what situation would cause this. Looking forward to getting help.
from Integrative Genomics Viewer User Guide (Paired-end alignments - IGV Desktop Application), when an inversion shows up in paired-end reads, there should be both RR reads and LL reads. As shown below.
When I use the orientation of Illumina paired reads to detect inversions, I found a region only have RR reads, see the picture below. I used color alignments by pair orientation, and view mate region in split screen. I don't know what situation would cause this. Looking forward to getting help.
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