IGV 2.10.2 alignment displays only the top 1200-ish reads (no downsampling)

11 views
Skip to first unread message

Grzegorz Piętka

unread,
Sep 1, 2021, 6:16:35 AM9/1/21
to igv-help
When I view a substantially well covered location or load several .bam files, the IGV window only displays the top 1200-ish reads and the rest of the alignment window is white. The last read is partially visible and there is a thin horizontal line as if there was an inner "alignment display window" inside the IGV panel. All of the reads appear to be still there as I can sort the visualization and don't get any error messages, I just can't see anything below the 1200-ish reads. I have the 8 GB memory option enabled.

I looked through the preferences, manual, FAQ and forums, but I can't find gow to solve this.



IGV alignment display issue.png

James Robinson

unread,
Sep 1, 2021, 10:48:36 PM9/1/21
to igv-help
Yes this is a known issue,  see https://github.com/igvteam/igv/issues/981.   There is a limit on the size of a graphic canvas in Java that is the root cause.   There is not an easy or obvious solution at this time.  You can "squish" the reads to see more.

IGV -Web (https://igv.org/app) does not have this limitation.  

Reply all
Reply to author
Forward
0 new messages