Help
About WebSeq/Logging In
WebSeq is a web-based system to deliver files to our customers. Currently, we provide sequencing, TaqMan, genotyping output files.
Access to this service is restricted to our existing customers and requires a login name and password. You (or your lab as a group) should have been given a login name and password upon signing up with the GenoSeq Core. If you would like to sign-up, have signed up in the past but do not recall your login and password, or have any other questions, please contact us at webseq@genetics.ucla.edu or by phone at 310-825-5488.
Please visit http://www.genoseq.ucla.edu for additional information about the GenoSeq Core and its services.
NOTE: The GenoSeq Core provides access to customer files via WebSeq for a limited time only (90 days for sequencing/TaqMan files, 30 days for genotyping files). Files older than 90 days will not be available through WebSeq. For recovery of older files, please contact us contact us at webseq@genetics.ucla.edu or by phone at 310-825-5488.
Files display & and filtering
Upon successful login, you will be shown a list of available files for your group. If you have set a preferred file type to show, this type will be displayed; otherwise the default is to show sequencing files.
The default list sort order is by file name; you can click on either the "size" or "date" columns to sort by those parameters instead. Size is sorted smallest first and date is sorted newest first. If, for a particular file type, there are more than 1000 files, then only the newest 1000 will be displayed. This is to prevent very large lists from slowing down and potentially crashing your browser. If the files that you want do not appear in this list, use the filter function to narrow down which files you want to see. If you wish to see the complete list, regardless of size, filter for a period character "." This filter will match all files, and there are no limits when a filter is used.
To use the filter function, enter a series of characters in the filter input box and click the Filter files: button. Only those files that contain that series of characters will then be displayed.
Downloading files
Take the following steps to download files:
- Select the file type you want to download by clicking on one of Sequencing, TaqMan, or Genotyping from the main menu.
- To download one file, click on that file's name. Your browser should then prompt you for a save location for this file. This file is not zipped, so it can be used directly.
- To download multiple files, check the selection box that appears next to the name of each file you wish to download. Then click the Download button. Your browser should then prompt your for a save location for this file archive, in zip format. Please see the zip section for help handling these files.
Selecting files
For convenience, you can use the Select All, Select None links to select all files or de-select all files, respectively. To select a range of files, select the first one in the range, then select the last one in the range, then click the Select Range button to automatically select everything between the two.
About sequence files
The sequence files made available here are recognized by a variety of programs. The following is a partial list of free software:
- Chromas
- FinchTV
- Sequencher
- We recommend Sequence Scanner from Applied Biosystems as it allows you to view the "raw" data which shows the amount of product produced from the sequencing reaction.
For a list of sequence alignment software, visit wikipedia
Tips for interpreting and troubleshooting your results.
About TaqMan files
The exported TaqMan "results file" can be opened with Microsoft Excel. The zipped raw data file can be downloaded and opened using Applied Biosystems SDS 2.3 software (for Absolute Quantitation and Allelic Discrimination analysis) and Relative Quantification (RQ) Manager software (for Relative Quantitation analysis). This software is available for GenoSeq Core users on the 4th computer from the left (Hg5301-3) in the Interaction Zone on the 5th floor of the Gonda Building. Please come see Core personnel if you need a Gonda Account to access your data on this computer.
About zip files
Due to inherent limitations of web technology, files downloaded from this site may be archived in zip format. Archiving files is the only way multiple files can be downloaded at once.
Note: zip archiving is used when you request a download of multiple files. If you select only one file for download, or you click the a single file name to download it, then it will not be zipped and you can use that file directly. If you attempt to unzip this file, you will probably get a warning that the zip file is corrupted, because it is not in the zip format.
Once you've downloaded these zip files, they must be unarchived (unzipped) in order to make use of the files again. Unzipping requires unzipping software. Fortunately, such software is ubiquitous.
Almost all Macintosh computers should have Stuffit Expander already installed. On Windows-based computers, unzipping software is not generally installed by default and must be installed separately.
Macintosh
All late model Macintosh computers ship with Stuffit Expander installed and the default browser configured to hand-off zip files to Stuffit Expander for automatic unarchiving.
When clicking a download link in WebSeq, you will be presented with a dialog asking where you wish to save the file. Click the Desktop button, and then the Save button. The file will download and save to your desktop and then Stuffit Expander will automatically unzip/unarchive the zip file. You should then find a folder on your desktop containg your requested files, which you can then use with your application of choice. You can delete the file named webseq.zip
If for some reason the zip file downloads but is not automatically unarchived by Stuffit Expander, check that your browser is configured to automatically hand the file off to Stuffit Expander. In Internet Explorer, go to Preferences and in the Network:Protocol Helpers panel, make sure the zip "protocol" is configured to use Stuffit Expander.
Once the files have been properly unarchived, you may wish to assign them the proper file type so that the operating system can associate them with a particular application. For sequencing files, download our MakeABI utility. Once uncompressed, you should have an application called MakeABI. Drag and drop your files onto this application and the file type codes will be set for you.
Error claiming zip file header is corrupt
Some users have experience this error when downloading/unarchving files from WebSeq. This occurs with older versions of Stuffit with buggy zip file support. To fix this problem, please upgrade to the latest version of Stuff.
Windows
Windows does not normally ship with an installed zip utility program and is therefore up to the user to download and install one. There are many to choose from - below are tutorials for two that are freely available to UCLA researchers: 7-zip (freeware) and TurboZip (site-licensed to UCLA). You may find that WinZip (shareware) has been installed on your computer - if so, consult WinZip support and adapt the directions below.
7-zip
We recommend 7-zip to our Windows users as it is simple and free. It can be downloaded from 7-zip's site.
If you are using Mozilla/Firebird/Netscape, select Save it to disk in the download dialog, then save the file webseq.zip to somewhere convenient, such as your desktop.
Likewise, if you are stuck using Internet Explorer, click the Save button in the download dialog, and point it at your desktop.
Once it is installed, 7-zip will automatically recognize zip archive files and label their icons with a blue "Z". To unarchive these files, right-click on them, and select Extract files.... You could also select Extract Here, but this will result in all of the files appearing all over your desktop. If you have downloaded 96 files, for example, this may not be desirable.
Finally, you'll be presented with a dialog asking to where you want to extract your files. Generally, the default is acceptable, so click the OK button. You should then have a folder on your desktop named "webseq" containing all of your files.
TurboZip
TurboZip is freely available to UCLA-affiliated individuals. To download TurboZip, register here and you will be presented with the passphrase required to install TurboZip. Note: a ucla.edu email address is required.
Once you have TurboZip installed, you will need to initially configure it. In the Folders panel of the configuration, set the Default folder to extract files to to your Desktop and make sure Automatically extract to selected folder is checked.
If you are using Mozilla/Netscape, select Open using TurboZIPX and the zip file will be opened by TurboZip.
If you are using Internet Explorer, the process is a little more involved. When first presented with the file download dialog, click the Save button (not the Open) button.
Then, when the second dialog appears, click the Open button. Internet Explorer will then pass the file to TurboZip.
Now within TurboZip, click the Extract button and your files will appear on your desktop. Quit TurboZip once it is done.