adding external tracks on the genome browser

Hi,
I have a question regarding the addition of external tracks on the genome browser. I am trying to upload some microrray data as an annotation track using the WIG format suggested in the “annotation file format” help. The link to the WIG file format description on the help page wasn’t working, but I found a description at : http://genome.ucsc.edu/goldenPath/help/wiggle.html

I tried to use their example:
track type=wiggle_0 name=“Bed Format” description=“BED format” visibility=full color=200,100,0 altColor=0,100,200 priority=20
chr19 59302000 59302300 -1.0
chr19 59302300 59302600 -0.75
chr19 59302600 59302900 -0.50
chr19 59302900 59303200 -0.25
chr19 59303200 59303500 0.0
chr19 59303500 59303800 0.25
chr19 59303800 59304100 0.50
chr19 59304100 59304400 0.75
chr19 59304400 59304700 1.00

replacing the "chrom chromStart chromEnd " values with C.elegans “chrom chromStart chromEnd values” creating the following file:

track type=wiggle_0 name="Bed Format " description=“BED format” visibility=full color=200,100,0 altColor=0,100,200 priority=20
I 4645631 4645672 1.0
I 4645790 4645720 0.75

When I create a “new annotation” from the genome browser page, and paste this in, it seems to register as a new track, but the annotations are not displayed correctly. I tried changing the landmark to chr1 or chrI also but that doesn’t work either.

Would you have any suggestions on how to fix the file format to display this?
Thanks,
Lisa

Hi Lisa,

You are on the right track, so to speak. Unfortunately, pasting in the wiggle data does not work but, if you save it as a file on your computer, then use the ‘Upload’ option, it should work.

There is some documentation on uploading wiggle track to gbrowse here:

http://gmod.org/wiki/index.php/Gbrowse/Uploading_Wiggle_Tracks

Regards,
Sheldon McKay

Hi Sheldon,
Thanks for your note. I’m using the WormBase genome browser. Should this matter? I tried saving the data as a file and uploading that ( tried both the example that I pasted below and also the example file from the GMOD docs) , but this doesn’t work.It appears that the input file is reformatted incorrectly after uploading. I’ve pasted below :

1.the first few lines of the file I uploaded
2. the file as it appears in the “external tracks” when I opt to “edit file”


uploaded file


track type=wiggle_0 name=“polyA” description=“mixed-stage polyA tiling array” visibility=pack altColor=0,0,255 windowingFunction=mean smoothingWindow=16
I 456 480 0
I 496 520 59
I 523 547 0
I 547 571 110
I 577 601 159
I 692 716 189
I 809 833 168
I 835 859 40
I 861 885 0
I 911 935 0
I 933 957 74
I 962 986 0
I 1037 1061 0
I 1068 1092 0
I 1096 1120 88
I 1120 1144 5
I 1174 1198 0
I 1223 1247 0
I 1249 1273 0
I 1272 1296 0
I 1324 1348 0
I 1349 1373 0
I 1372 1396 51
I 1399 1423 78


file as appears in external annotation track


[track001]
glyph = wiggle_density
key = polyA
description = mixed-stage polyA tiling array
fgcolor = black
bgcolor = blue
smoothing = mean
smoothing window = 16

reference=
track001 .data … Name=polyA;Note=mixed-stage%20polyA%20tiling%20array;wigfile=

reference=I
track001 I.data 457…766508 Name=polyA;Note=mixed-stage%20polyA%20tiling%20array;wigfile=/var/tmp/ace_images/gbrowse/vab/elegans/uploaded_file/b9fb6b1462dcdcbddaa93db03b96f16e/track001.I.1211287341.wig

Sorry if I am somehow missing something obvious!
Thanks,
Lisa

Hi Lisa,

There was a bug on the wormbase installation. It is fixed on the development site. The link below shows an uploaded wiggle track using the example file from the GMOD wiki:

http://tinyurl.com/4kw7z7

Please use dev.wormbase.org for now. The above example uses a remote URL rather than a file upload but, for uploads, you can adjust how the track looks by changing the smoothing, min and max score, etc either in your wiggle file or using the ‘edit’ button after you upload. If you wiggle track still fails to work as you expect, please email me the complete file at mckays@cshl.edu and I will have a look.

Sheldon

Hi Sheldon,
Thanks very much, that worked! I just had one other file format question. I would like to add a URL to which the annotations in the track will link and I had understood that this could be done either by including the URL as the 5th column in the file like this:

[expression]
glyph = xyplot
graph_type=boxes
fgcolor = black
bgcolor = red
height=100
min_score=0
max_score=110
label=1
key=Expression Level

reference=I
expression liver 10000…12000 score=10 http://www.google.com
expression liver 12001…19999 score=50 http://www.google.com
expression liver 20000…25000 score=100 http://www.google.com

or by adding the URL in the configuration section like this:

[expression]
glyph = xyplot
graph_type=boxes
fgcolor = black
bgcolor = red
height=100
min_score=0
max_score=110
label=1
key=Expression Level
link= http://www.google.com

reference=I
expression liver 10000…12000 score=10
expression liver 12001…19999 score=50
expression liver 20000…25000 score=100

But neither of these options seems to make the link work. The annotations shows up fine though.
Thanks again for your help and the documention for this (and the new Generic Genome Browser: A Tutorial) is just great!
Lisa

Hi Lisa,

This does not work for me either. I will have to investigate…

Sheldon