Downloading Sequences and Chromatograms

Important Notes

We maintain files on our servers for approximately six months, depending on demand. Please download your sequence files to your own machines to work on them, as files will be purged from the server periodically. We also ask that you disconnect from the server as soon as possible to prevent saturation of our server connections. We maintain backups of all data we generate on CDs.

Please be aware that the text sequence provided to you should be considered 'raw' sequence. It is necessary to view the chromatograms to correct (usually) minor errors and make reasonable judgements of where to trim the sequences. Please look at representative chromatograms here for more information.

Files can be downloaded three ways:
1) Filesharing (Macs & Windows, local or remote access)
2) FTP transfer
3) Web browser (slowest but some pitfalls).

Filesharing (Macintosh Internal users only)

From the Finder on a Mac, click on the "Go" menu, and choose "Connect to Server" at the bottom. Type in the server name "DNACore.bsd.uchicago.edu" to connect. Login using your assigned username and password. Navigate to your own folder in your lab's directory. Click and drag the appropriate files to your disk. DO NOT open the files from the server directly. Disconnect from the server as soon as you have transferred the files. A useful shortcut is to make an alias to your lab's folder by selecting it in the Finder and choosing "Make Alias" in the File menu. This alias can then be used to make a faster connection directly to the lab's folder in the future.

Filesharing (Windows Internal users only)

In Windows XP choose "My Network Places" from the start menu. In the next window choose "New Network Place" from the left pane to start the wizard. In the Wizard, click next, then pick "Choose another network location". In the next window in the address field type \\DNACore.bsd.uchicago.edu\username where "username" is your own username. In the popup window that comes next (there may be some delay), type in your username and password. In the following window choose a name for the new network place (like DNA Sequencing Server). Navigate to your own folder in your lab's directory. Click and drag the appropriate files to your disk. DO NOT open the files from the server directly. Disconnect from the server as soon as you have transferred the files.

FTP transfer

On Windows, Macs and Unix you can use FTP client software such as Filezilla (download from http://filezilla-project.org/download.php). Connect and login using the information originally provided in your first e-mail of results, making sure to use the correct case of the username. You will need to change the preferences so binary transfers are the default transfer choice for files lacking extensions (low throughput chromatograms lack the ".ab1" extension due to our editing), since chromatograms are binary files. This setting is found under the "File Transfer" dialog and is a checkbox that needs to be unchecked ("Transfer files without extensions as ASCII"). The .seq files are plain text.

Web Browser

For Low Throughput results only using web browsers that do remember passwords (NOT Internet Explorer!), fill out the following form (using the proper username case) and press submit:
Server machine
DNACore.bsd.uchicago.edu (internal users)
CRC-DSF.uchicago.edu (external users)
Username:

For High Throughput results and if you cannot connect using this method (eg. certain web browsers don't automatically request a password), you will need to enter your information manually. Please edit the URL that is pointing to this page in your browser, or choose the option to open a new location and type or paste in one of the following, depending on which server your files are on (make sure the username case is correct):

ftp://username:password@CRC-DSF.bsd.uchicago.edu/          (external high & low throughput)

ftp://username:password@DNACore.bsd.uchicago.edu/          (internal high & low throughput)

A directory listing should appear. If necessary, navigate into the Users directory, then into your lab or institution's directory, and finally into your specific directory. Sequences will be displayed as plain text documents and chromatograms as document files. Click on any file to download it. NOTE! If you only see old files and your new results don't appear, please refresh the page (you may need to hold down the alt/option key too) since web browsers often cache directory views. If they still don't appear, contact us at 773-702-1088.

If the .Seq file appears as a single long string of characters in the Web browser window, you can modify your browser to automatically save it as a text file instead. Open the preferences menu and choose the "Helpers" option (or equivalent). Choose "New" to define a new type, naming it "DNA sequence file", and setting the MIME type to be "TEXT/plain". The suffix should be "Seq". Then choose the handling to be "Save to Disk" and click OK.

Problems

If you have problems with your web browser showing old directory information, you will likely need to force a directory update by holding down the alt/option key and clicking on the refresh button. If you encounter problems connecting, viewing or downloading your files, or if you wish to change your password, please contact the Core (773)702-1088.