IGV BED File Color Display

1,657 views
Skip to first unread message

jpu...@broadinstitute.org

unread,
Jul 28, 2015, 1:45:37 PM7/28/15
to igv-help
Hi,

I am using IGV 2.3.55. I am uploading peak BED files from MACS 2.0.9, and I want to change the color of those to match the bedgraph track they associate with. However, it will only let me change positive value colors and this doesn't actually change the color of the bars. How do I properly change those colors?

Best,
John

Jim Robinson

unread,
Jul 28, 2015, 1:53:33 PM7/28/15
to igv-...@googlegroups.com
If its a bed file (as opposed to a bedgraph file)  right click and select "Change Track Color...

You can also set the color explicitly in the file with a "track" line.


--

---
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/2da87c05-dea8-40fa-a36c-e9240b29f96c%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

John L Pulice

unread,
Jul 28, 2015, 1:56:39 PM7/28/15
to igv-...@googlegroups.com
Hi Jim,

I have done that and it doesn't change the displayed color of the bed file. If I go back to edit the track color again it saved the new color but it's not changing the displayed BED color: The top A549 row is what the opened color tab is for, and it was already saved and reopened to show this.

John

Inline image 1

--

---
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/TcD-tuMAxZw/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/55B7C199.3080703%40broadinstitute.org.

Jim Robinson

unread,
Jul 28, 2015, 2:02:00 PM7/28/15
to igv-...@googlegroups.com
Could you attach the bed file?  Not the whole thing just the first 10 or 20 lines.  Its possible colors are set explicitly in that file for each individual feature,  if that's the case changing the color of the track won't overwrite it. 

Jim

John L Pulice

unread,
Jul 28, 2015, 2:03:49 PM7/28/15
to igv-...@googlegroups.com
Hi Jim,

Here you go:
Inline image 1
Best,
John

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/55B7C393.70201%40broadinstitute.org.

Jim Robinson

unread,
Jul 28, 2015, 2:05:06 PM7/28/15
to igv-...@googlegroups.com
John,  could you actually attach the file,  I can't load a screenshot.   I think the problem is with the "0" in the color file,  0 == black,  although I want to load it to be sure.

Jim

John L Pulice

unread,
Jul 28, 2015, 2:20:36 PM7/28/15
to igv-...@googlegroups.com
Yep that's it, the itemRgb column was all 0s. I change it to the proper RGB color and it works now! Thank you!

Best,
John

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/55B7C44E.6080304%40broadinstitute.org.

Jim Robinson

unread,
Jul 28, 2015, 2:22:13 PM7/28/15
to igv-...@googlegroups.com
OK,  that's still an igv bug,  the column shouldn't take effect unless itemRGB="on" in the track line.   I guess the default is on,   I'll change it to "off" for the next release.   In the past I've seen "." used in that column,  which I'm pretty sure igv ignores.

Jim

Reply all
Reply to author
Forward
0 new messages