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Old 01-31-2012, 08:18 PM   #1
Alexander Tchourbanov
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Location: Las Cruces, NM

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Posts: 10
Default GFF3 display in IGV

Dear colleagues,

I am trying to display the variants annotations along with predictions of exonic aberrant isoforms in IGV and can't make it to display color. Moreover, only gene field in the GFF3 last description column is actually used for display, which I would like to replace with the field like note=... Is there way to make it better (I though using track description may help but so far it didn't)?

Code:
##gff-version 3
#track name="Aberrant splicing" color=FF0000 gffTags=on
chr10	varclass	splicingVariants	100018766	100018821	.	-	.	Var=0.1->0.07;gene=Overlapping exon change (0.1->0.07);ref=novel;InRegion;color=FF0000
chr10	varclass	splicingVariants	100018844	100018844	.	+	.	Var=G->A;gene=G->A;ref=novel;InRegion;color=FF0000
chr10	varclass	splicingVariants	100018766	100018832	.	-	.	Var=0.07;gene=Exon compromising is created (0.07);ref=novel;InRegion;color=FF0000
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Old 02-11-2012, 07:34 AM   #2
Jim Robinson
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Default

Hi,

First IGV has a help forum where you are more likely to get a timely response, the URL is https://groups.google.com/forum/?hl=...forum/igv-help

A couple of points (1) you don't need the "gffTags" in your track line, that is for using gff tags in bed files (2) your color strings need a if you use a hex number, for example #FF0000. I'm not sure what you mean by "used for display", its used to label the feature but if you mouse over it you will see all the attributes. I assume you are using IGV 2.0 or 2.1.

-- Jim
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Old 02-12-2012, 11:31 PM   #3
Alexander Tchourbanov
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Location: Las Cruces, NM

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Thanks for the good hint regarding use of # before color code, it works! The working link to IGV group discussion is http://groups.google.com/group/igv-help/.

At the GFF3 display page for IGV browser
http://www.broadinstitute.org/igv/GFF
we have the following recommended format

Code:
##gff-version 3
chr1 varclass variants_454HCDiffs 59133 59133 33 . . Var=A->G;AA=S->S;depth=9;frame=+1;gene=OR4F5;ref=novel;InRegion;color=0000EE
chr1 varclass variants_454HCDiffs 59374 59374 67 . . Var=A->G;AA=T->A;depth=30;frame=+1;gene=OR4F5;ref=rs2691305;InRegion;color=EE0000
chr1 varclass variants_454HCDiffs 731442 731442 100 . . Var=T->C;AA=->;depth=3;frame=;gene=;ref=rs3115865,rs61770168;OutOfRegion;color=AAAAAA
That is why I made this mistake. By display I mean that only gene=G->A is displayed as label underneath a glyph (but this is not a gene annotation). I wish I could have more flexible way of annotating my glyphs, but at this point I don't have a clue how to accomplish it.

Last edited by Alexander Tchourbanov; 02-15-2012 at 03:14 AM.
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