Alignment view for PacBio reads

[Nicolas Marcel Alexandre PhD]

Hello,

In a previous instance where I used IGV, I aligned raw PacBio reads to a genome to view a deletion. As you can see, there is a 30 KB deletion in the linked read view with supplementary alignments (split reads) on either side of the deletion (See attached PacBio_Deletion.png).

Now, everytime I open IGV and view the same region using the same input data, I can no longer view this in the same way. I only now see stacked alignments without the split alignments (See attached Error.png). If I could get help changing my preferences to regenerate the first figure, I would greatly appreciate it.

Nicolas

[Nicolas Marcel Alexandre PhD]

This is for IGV_2.11.1.

[robin...@gmail.com]

Hi Nicolas,

I'm a bit confused by your screenshots.  The one labeled "PacBio_Deletion" actually shows a 2 base insertinon ("AG") that is expanded.   I don't see any deletion or split alignments, and you would definitely not see a 30kb deletion in a window 40 bp wide.  I don't see any split reads in the screenshot labeled "Error.png", but there is an insertion which could be expanded using the purple triangular controls just under the coverage track.