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
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
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:
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
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:
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.
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
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