IGV show no alignments

[Roman Vasilyev]

Dear IGV Support Team,

I've encountered peculiar problem with IGV v 2.3.88. It shows blank pages on highest zoom, although it worked well a moment ago. I tried to open about a dozen files I know it displayed correctly in this session, but they all show up blank. 

I tried relaunching IGV, restarting PC and re-installing IGV. No effect. Checked what reference genome is currently set - it was alright. What should I do next?

Best regards,

Roman Vasilyev

[Helga Thorvaldsdottir]

Hi Roman,

We'll need some more info to help diagnose your issue. It would be helpful to get a screenshot that shows the problem, and your igv.log file from <your home directory>/igv, and ideally also a sample bam file that displays this behavior (or even better if you can reproduce it with a bam file from the IGV "Load from Server" menu). A common reason for no alignments showing up is viewing the bam file with the wrong reference sequence (ie a mismatch between sequence names in the bam and reference), but it sounds like that's not what's going on here.

Helga

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[Roman Vasilyev]

Dear Helga,

Thank you for your kind reply. I don't know what exactly has changed, but seems like everything is in order now.