bedGraphtobigWig

[TOSTI Luca]

Dear UCSC,

I tried to convert a bedgraph file to bigWig using the bedGraphtobigWig tool, however when I upload the file I get this error:

"    Error File 'test.bigWig' - It appears that you are directly uploading binary data in an unrecognized format. For custom track formatting information, please see custom track documentation.”

Could you help me somehow?

I attach the file I used, I kept only two lines. The command I typed in was:

c000195:BED_conversion luca-laptop$ ./bedGraphToBigWig test.bedGraph mm10.chrom.sizes test.bigWig

Many thanks for your help,

--

Luca Tosti, MSc

PhD Candidate
Biology of Reprogramming
MRC Centre for Regenerative Medicine
SCRM Building
University of Edinburgh,
Edinburgh BioQuarter, 5 Little France Drive,
Edinburgh, EH16 4UU
UK

[Jonathan Casper]

Hello Luca,

Thank you for your question about loading a bigWig file into a custom track for the UCSC Genome Browser. It sounds like you're trying to upload the file as a custom track using the "Choose file" button on our custom track CGI at http://genome.ucsc.edu/cgi-bin/hgCustom. If so, then the problem is that we do not support loading bigWig custom tracks that way. To load a bigWig custom track onto the UCSC Genome Browser, you need to provide a URL to the file at an http, https, or ftp location. UCSC will then download pieces of that file as needed for display. More information on this process is available at http://genome.ucsc.edu/goldenPath/help/bigWig.html.

Please note that while the discussion on that page suggests building a track line to allow you to configure the track, that is not strictly necessary. If you just paste the URL of your bigWig (e.g., http://myorg.edu/mylab/myBigWig.bw) into the custom track text box and click the Submit button, the track will be loaded with default settings.

If you are not able to place your bigWig file somewhere accessible via URL, then you will need to use another file format like the bedGraph from which your bigWig was derived.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

--


The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

--