Wig file interpreted as bed file in genome browser

Question

[salamandra]

Hi,

when uploading wig file into genomebrowser the file is read as a bed file, only bars are shown in the intervals, no peaks are shown.

Did this happen before to anyone? How did you solve?

[GenoMax]

Make sure you WIG file is in correct format. Post the header and the few lines from your file.

[salamandra]

it's in binary format, can't look inside it

[salamandra]

but here goes few lines of bedGraph, also being read as a bed file by genomebrowser:

chr1    0   5100    0.00
chr1    5100    5140    0.00
chr1    5140    5232    0.00
chr1    5232    5406    0.00
chr1    5406    7035    0.00
chr1    7035    7382    0.00
chr1    7382    8445    0.00
chr1    8445    9446    0.00
chr1    9446    9557    0.00
chr1    9557    9566    0.00

[GenoMax]

I will refer you back to the link above which describes what a Wiggle file should look like. You seem to missing the track definition line.

Answer 1

[genecats.ucsc]

As genomax said, you need to add a track definition line when you load your custom track, something like:

track type=bigWig name="Example Name" description="Example Description"
http://url.to.your/file

Here's a list of the different track types supported:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#format

and some of the many different "track fields" supported:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK

If you have further questions about UCSC data or tools feel free to send your question to one of the below mailing lists:

• General questions: [e-mail]
• Questions involving private data: [e-mail]
• Questions involving mirror sites: [e-mail]

ChrisL from the UCSC Genome Browser