Downloading Sequences and Chromatograms

Last updated on Oct 7, 2013

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) Web browser (recommended)
2) FTP transfer in a web browser
3) FTP transfer by client program (eg: FileZilla).

Web Browser

Web browsers (Safari, Chrome, Firefox, etc) can now be used to download individual files, several selected files, or entire folders (directories). Connect to the site http://DNAftp.uchicago.edu:8000/ and provide the username and the password that was provided to your lab at an earlier date (NOT your CNET id). This should connect you within your lab directory. Click on folders to enter them, or on the download arrow to transfer them. Multiple single files can be selected using the checkbox on the right, then downloaded using the download button on the bottom of the screen. Note that multiple files will be transferred as a zip file archive.

FTP transfer in a web browser

A web browser can be used to transfer individual files using FTP by connecting to this address: ftp://DNAftp.uchicago.edu/. Provide your username and password that were given earlier (NOT your CNET ID) to connect. You will be able to transfer single files at a time.

FTP transfer by client program

On Windows, Macs and Unix you can use FTP client software such as Filezilla (download from here). Connect and login using "DNAftp.uchicago.edu" as the host address, and then your username and password provided your lab earlier (NOT your CNET ID). You will be able to transfer individual files, multiple selected files, or whole folders, usually by dragging them from one window pane to another. Note that for first time users of Filezilla, 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.

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.