refseq genes not displaying all transcripts

[paul]

Hi,

I'm using IGV (ver 413 from 1/27/2016) on Windows 7. When I load the mouse mm9 or mm10 genome and look at the E2F3 gene, the Refseq annotation track only shows one transcript (I have "expanded" selected). However, if you look at the UCSC genome brower's RefSeq track, there are two E2F3 transcripts (I'm showing mm10 below and here is the link)

Why is this occurring?

A second related question is this: how does one create their own "RefSeq" track for a given genome? For example, IGV does not have the Hamster genome available. So how do I load the Hamster genome and have it show a RefSeq track at the bottom just like I see with mm9 and mm10?

Thank you,

Paul

[Jim Robinson]

Thanks for the report.  I just updated those annotations,  please try again.

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[paul]

Hi Jim,

After restarting IGV and trying both mm9 and mm10, I still only see one transcript for E2F3

Figuring that my mm9 and mm10 genomes aren't working, I went to Genomes->Load Genome From Server BUT I do not see mm9 nor mm10. I only see mm7 and mm8. What happened to mm9 and mm10? Maybe I should reinstall IGV? 

Thank you,

Paul

[Jim Robinson]

First remove them using "Manage Genomes",  then they will appear on the server list again and you can download them.  I suspect your local cache is not being refreshed.

Jim

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/3dfe4e7b-9a5d-4b20-924a-e3fa7b027c96%40googlegroups.com.

[Jim Robinson]

Another way to force a refresh is to delete the genome files from <user home>/igv/genomes, then start (or restart) IGV.

[paul]

Hi Jim,

This worked...thank you,

Paul