load GEO bigWig file into UCSC custom track

[Fred Mills]

Hello,

I'd  like to load the url for a GEO bigWig (bw) file via the add custom track field.

The url is 

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1329660&file=GSM1329660_RelA.bw

I've tried this, as well as 

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1329660&is_ftp=true&file=GSM1329660_RelA.bw 

as per a response from UCSC browser support in a Google UCSC Browser group from 2010; i.e.

https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/GEO$20url$20UCSC$20browser$20track/genome/SFYj8LeqRmQ/xakyZeyymMUJ

in both cases, I get the following error message:

Error No Content-Length: returned in header for http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1329660&is_ftp=true&file=GSM1329660_RelA.bw, can't proceed, sorry

Thanks very much  for any help.

Best,

Fred Mills

Staff Scientist

OBP,Division 4, CDER, FDA

Building 52, Room 2108

FDA Campus

10903 New Hampshire Ave.

Silver Spring, MD 20993

work email

frederi...@fda.hhs.gov

[Matthew Speir]

Hi Fred,

Thank you for your question about loading GEO data using a URL. The GEO URLs that you provided in your email go directly to an HTML page that describes that GEO accession number, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1329660. The URL to the file on NCBO's FTP server can be found at the bottom of the page under the "Download" section for the correct "Supplementary File". To get the URL that you can use to upload this GEO accession as a custom track, right-click the "ftp" link under the "Download" section for the " GSM1329660_RelA.bw" file and select "Copy Link Address" (this is true for Chrome, but may be labeled differently in other web browsers). You can then paste that URL into a track line used to upload custom tracks:

    track type=bigWig bigDataUrl=ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1329nnn/GSM1329660/suppl/GSM1329660_RelA.bw

You find information on configuring your custom tracks here:

• http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TRACK
• http://genome.ucsc.edu/goldenPath/help/bigWig.html
  

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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