trouble view mitochondrial chromosomes for mm10

[Haley Abel]

I am having trouble viewing the mitochrondrial chromosome for mm10, using IGV version 2.16.0.  My genome reference uses the name 'MT' for the mito chromosome vs the official igv grcm38/mm10 version, which uses chrM.  

I have downloaded the zipped reference bundle for mm10, created an alias file, and loaded this new genome into igv.  It loads, the genome shows up in the drop down, but I am not able to see any data on the MT chromosome.

I have also tried creating a complete new genome, using chromosome names 1-19,X,Y,MT.  That also did not work.  'MT' appeared as a choice in the drop down menu for chromosomes, but when I tried to choose it, I got a NULL chromosome error.

Thanks,

Haley

[igv-help]

This is not an alias issue, "MT" is already recognized as an alias for chrM.   Are you sure your data file contains data on MT?

I'm not able to comment explicitly on version 2.16.0, 2.17.4 is the current release,. othing has changed AFAIK wrt MM10 aliasing, but you might try the latest release.

[igv-help]

My other suggestion would be to force a refresh of your mm10 genome by selecting it again from "Genomes > Select Hosted Genome..."

[Haley Abel]

Thank you!  You are correct--I did not realize that MT had been removed (not by me!) prior to creation of our bigwig files.

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/z9dS8ZGVzX8/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/120b68f1-6b26-424d-9634-8c7c5c0fad93n%40googlegroups.com.