problem loading custom tracks
Trumbly, Robert
I am unable to load custom tracks by copying the urls of bigwig files from GEO. I have previously used this method successfully. The error message is shown in this screenshot: error loading GEO wig file as custom track. Since I couldn’t diagnose the problem, I used the example file provided on your website. I got a different error message. I have attached a screenshot: error loading custom tracks.
I would appreciate your help. I am using a method I used previously.
Thanks,
Bob Trumbly
Brian Lee
Dear Bob,
Thank you for using the UCSC Genome Browser and your question about accessing custom tracks at GEO.
Thank you for taking the time to investigate the issue and sharing your experience with our documentation link. A quick test shows it is working, however, I did replicate your experience when my copy and paste buffer included an extra whitespace character on the end of the URL to the "bigBedExample.bb " file. You may want to check if that was the issue for that URL and the other GEO-hosted file.
Looking closely at the screenshots, thank you for including them, it also appears the URL from GEO that you are trying to load is not a file location: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM2359435
You want to find a file that likely includes an ftp in the link and ends with "bw" for bigWig or in this case, WIG.gz: https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2359nnn/GSM2359435/suppl/GSM2359435_20160603_4845.7212.rpm.WIG.gz
A test of using this URL works (the below is the equivalent of pasting in the URL as a custom track), and hopefully should resolve the issue: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031935-33041243&hgct_customText=https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2359nnn/GSM2359435/suppl/GSM2359435_20160603_4845.7212.rpm.WIG.gz
You may be interested in learning about how bigWig files are ways to host and share data in the WIG format that allow you to retain control of the files by converting them into binary-indexed formats and hosting them on a website: http://genome.ucsc.edu/goldenPath/help/bigWig.html
Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
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