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LocusZoom - Frequently Asked Questions

General questions:

This service is "not actively maintained". What should I use instead?

The service is not actively maintained, and lacks some features relevant to modern usage: the support for large plots is limited, and annotation information (eg genes) does not reflect the newest reference datasets in the field. There is also no support for datasets in newer genome builds such as GRCh38.

We recommend using our new site for the latest features, including Manhattan and QQ plots, support for build GRCh38, and interactive ways to explore the entire dataset from a single file upload.

We are continuing to add features to the new service. In the interim, the old service will continue to be provided as a courtesy, but it is not actively maintained and support is limited.

Why does this project exist?

We wanted to provide a tool that people could use to generate their own regional plots, and have the ability to manipulate options to change the way the plots look.

Will my files be kept confidential?

Your results files will be kept completely confidential in a secure location and will be deleted immediately after plots are generated.

How long does it take to generate a plot?

Interactive plots Using Lipids GWAS Results generally take 10-30 seconds to generate a plot. Plots using data provided by you can take much longer. The plotting portion takes less than a minute. All of the extra time you see is due to network delays in copying your data to the server. You'll be much happier if you compress your data before uploading it (see the compression question).

How much of my data can I plot?

The LocusZoom server currently accepts files of 2GB or less. We recommend that you compress your data before uploading it (see the compression question).

How can I compress my data to make the plotting faster?

When plotting your data, most of your wait is due to network delays as your data is copied to the server. You can usually reduce the size of your data by a factor of 3-10 times by compressing it. On Linux/Unix/Macintosh systems, open a terminal and enter the command:

      gzip myfile
This will create the file 'myfile.gz' which you should provide to the web browser (Path to Your File). On Windows systems use the freely available program 7-Zip (or Winzip if you have that installed). Do not combine multiple files together - they will not work.

What does 'Unable to find the file information on the server' mean?

Sometimes when you attempt to upload data to the server, it will fail with a vague message like Unable to find the file information on the server. Uploading a file can fail for any of these reasons:

  1. The file was too large (most likely case).
  2. The server disk space was filled (not caused by your file) This is very unlikely.
  3. The network connection failed somewhere between the server and your machine. This is very unlikely.
  4. The LocusZoom software has a bug (very unlikely we hope).

Look to see how large the file is. If it is larger than the limit documented on the web page (5GB), compress the file and try again.

I can't seem to get my input to generate a plot. What to do?

A plot may not generate if the SNP name or gene name cannot be found. Please double-check the gene name exists in the UCSC browser before requesting a plot based on gene name. Alternatively, please check the error message returned when a plot cannot be generated. If you still can't determine why the plot failed, ask for help on our message board or submit your issue via email.

What does 'Secure Connection Failed' or 'You have received an invalid certificate' mean?

Since you will be entering data that could potentially be stolen as you send it to our servers, we have chosen to use a secure protocol (https). This can lead to you get a warning from your browser saying something about Secure Connection Failed. It will probably mention you have received an invalid certificate. This messages does not normally appear anymore, but if your browser does not recognize the certificate authority used by the University of Michigan you could possibly see this.

All you need do is get the certificate and approve it permanently and then you will no longer see this warning. The exact details of how you do this will vary based on the browser and version you are using. Sorry for this hassle, but we figured you'd rather have your data be secure so we made this choice.

If you have no idea what this is about, these links might shed some light:

Locuszoom works in all cases except for this one option. What to do?

While it is always possible there is a bug in our code, another possibility is that we have made a change in the HTML and your browser has cached the old version of HTML, causing the problem. To check if this is the case revisit the page and press the shift key and then click the reload/refresh button at the same time. This commonly forces the web page to be reloaded - getting you the latest HTML from our site.

If this does not fix the problem then you can post your issue on the LocusZoom forum or submit your issue via email. Be sure to copy/paste all the messages you see, and include the operating system and browser you are using.

Frequently Asked Questions
LocusZoom Message Board
Report problems via email
Copyright © 2009- University of Michigan, Department of Biostatistics, Center for Statistical Genetics