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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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Split screen by supplementary alignments #738

Closed jrobinso closed 1 year ago

jrobinso commented 4 years ago

See #298

ryan-moreno commented 1 month ago

I am trying to access this feature and am having difficulty. Based on #1278, my understanding is that if I right-click on an aligned read that has a supplementary alignment tag, then I should get the option to split screen. However, this is not among the options I'm seeing. I have used various preferences and tried to find documentation for this feature, but have not found the solution. My use case is that I want to view the two regions surrounding the ends of a translocation and see which reads span the translocation. I can pull up the two regions in split screen manually, but using "Link supplementary alignments" doesn't seem to work across split screen. Any suggestions?

jrobinso commented 1 month ago

What version of IGV are you running?

jrobinso commented 1 month ago

And linking (as in drawing a connecting line) will not work across split screens, they are completely independent.

ryan-moreno commented 1 month ago

I am using 2.16.0. Happy to provide log files if that is helpful.

jrobinso commented 1 month ago

I'm not entirely sure what you are trying to do, but there are a number of features for split reads in the latest version (2.18). See https://igv.org/doc/desktop/#UserGuide/tracks/alignments/chimeric_reads/. I do not recall exactly what was in 2.16 in this regard.

ryan-moreno commented 1 month ago

Those were the exact features I was looking for, thank you. Sorry I did not think to check if I was using the older version 🙈