search

igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
646 stars 387 forks source link

"Read Order" is wrong in "Supplementary Reads Diagram" #1550

Closed simondrue closed 2 months ago

simondrue commented 2 months ago

Hi,

First, thank you very much for the very useful "Supplementary Reads Diagram" feature. If understand it correctly, the order in the vizualization in the "Read Order" pane is reversed. Here are two examples for a forward and reverse read:

Reverse read image

Forward read image

Thanks for a great tool,

Kind regards, Simon

jrobinso commented 2 months ago

Hi Simon. Its impossible to say from screenshots, what makes you think it is wrong? Have you examined the reads sequence and SA tag?

simondrue commented 2 months ago

Hi @jrobinso,

After looking at some more examples i must admit i misunderstood the figure. In my mind the in the read order pane the read should be shown always from left to right, i.e. all "parts" of the read pointing to the right. I understand now that its the order of the parts in the read, but shown in the direction of the alignment.

Tanks again for a great feature - looking forward to getting to know it better.

I'm closing the issue.

/Simon