problem exporting junctions.bed file

Lynn Amon

unread,

Sep 28, 2015, 1:44:45 PM9/28/15

to igv-help

I am having trouble exporting the junctions bed file from IGV. I loaded a bam file for RNA-seq data that results in the bam track and coverage and junctions tracks. I right click on the junctions track and click 'Export Features...'. I am prompted for a file name and I hit return. The file gets created but it is empty. Am I missing something? Does anyone else have this problem?

Version 2.3.60(87)
OS: Linux Ubuntu 12

Thanks,
Lynn

Jim Robinson

unread,

Sep 28, 2015, 6:15:24 PM9/28/15

to igv-...@googlegroups.com

Thanks for the report. I was able to reproduce this, it is a bug. I will update this thread when a fix is available. Apologies for the inconvenience.

Jim

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, 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/408c9994-1436-448b-803c-16cdf3313c8b%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Jonathan Rupp

unread,

Nov 24, 2015, 6:30:46 PM11/24/15

to igv-help

Thanks for working on it. I am also having this issue. Do you know if there is a workaround?

Cheers,

Jonathan

Jim Robinson

unread,

Nov 24, 2015, 6:34:10 PM11/24/15

to igv-...@googlegroups.com

No workaround, but I will release a fix this week, which for me ends tomorrow. I'll update this thread when its available.

Jim

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/aee541cc-cc11-4b8e-b488-af9d889bd240%40googlegroups.com.

Jim Robinson

unread,

Nov 26, 2015, 12:46:47 AM11/26/15

to igv-...@googlegroups.com

This is now fixed in the development snapshot build here: http://www.broadinstitute.org/software/igv/download_snapshot. The fix will be included in the next release, early next week.

Jim

On 11/24/15 3:30 PM, Jonathan Rupp wrote:

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/aee541cc-cc11-4b8e-b488-af9d889bd240%40googlegroups.com.

Jonathan Rupp

unread,

Nov 30, 2015, 10:01:03 PM11/30/15

to igv-help

Works great, thanks.

j

Jim Robinson

unread,

Nov 30, 2015, 10:02:54 PM11/30/15

to igv-...@googlegroups.com

OK, I'll be releasing this tonight with version 2.3.64.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/d4482ceb-25cc-4554-88b4-da91e3c98f36%40googlegroups.com.

Reply all

Reply to author

Forward

Message has been deleted