How do I download and view my chromatograms?

In order to download and view your chromatogram files, there are three steps to follow:

I will discuss each of these three steps in order.


1. Obtain a Program That Can Open Chromatogram Files

Chromatogram files are NOT in a 'standard' graphics format. You cannot open them with GIF
or JPG viewers, or Photoshop or whatever. They are data files specific to DNA sequencing,
and you need specific programs that understand the raw data in these files and understands
how to present it as a four-color graph.

There are many programs that can do this, and many of them are free or inexpensive shareware.
Some of the best ones are costly but are very feature-rich and capable.

Programs that can read DNA sequencing chromatogram files include:

Free Programs for Typical Desktop Computers:

Sequence Scanner Software 1.0 from Applied Biosystems, Inc.

A free program for viewing or printing chromatograms for the PC. You can get it directly from ABI
by clicking on the link above. Yes, I know it's odd to see 'free' and 'ABI' in the same sentence!
This one will print your chromats, allow you to edit them, or export the text sequence to other
programs. It is especially usefull for scanning lots of chromats fast.

4Peaks from Neefix Laboratories.

A VERY nifty (and free!) program for viewing, editing or printing chromatograms, for the OS X Macintosh
ONLY. It does some cool peak-smoothing to make the traces look very clean. Plan on publishing a chromat?
Use this software to make the final figure! Thanks, Neefix, for this excellent program.

(In my experience, the print-outs aren't as nice as some other programs, but the beautiful on-screen display
is the biggest benefit of this program.)

EditView from Applied Biosystems Inc.

A nice, free program from ABI for viewing, editing or printing chromatograms from the Macintosh. You
can get it directly from Applied Biosystems by clicking on this link or you can download this program from
our own server by clicking here. When you are asked for a password, it's 'editview'.

Chromas

Chromas, by Conor McCarthy, runs under the various flavors of Windows (3.x, Win95, 98, NT, XP). The
page above is the Chromas Home Page. If you have trouble with that link, try the following:
http://brcweb.bio.cornell.edu/SoftwareArchive/Info_Chromas.html

ABIView

Written by David H. Klatte to allow PC users to view chromatograms. Simple and cheap!

TraceViewer

The people who sell phred and phrap (see below) have set up a company that also distributes TraceViewer,
a chromatogram viewer that is free for academic users. Versions are available for Windows, Mac and Unix.

Large packages (typically for server-class systems) that include chromatogram viewing:

The Staden Package

A suite of Unix-based programs for sequence data management.

The phred/phrap/consed suite of programs:

Industrial-strength shotgun sequence assembly software from Phil Green, Brent Ewing and David Gordon.
This package is used by many of the major genome centers. Prospective commercial users can also go to
a commercial site, http://www.codoncodes.com, to obtain these programs, and others from the same people
(e.g. see TraceViewer, above).

Commercial Packages for Typical Desktop Computers:

ABI's Sequence Analysis program

A very expensive program. Use it only if you have your own sequencer.

Sequencher from Gene Codes, Inc.

a very good sequence assembly program, with versions for both the PC and the Macintosh. This allows the
user to view chromoatograms during shotgun assemmbly. Please click here to learn why sequence assembly
is easier with a program that can use chromatograms.

Lasergene from DNAStar:

This is a very complete DNA analysis package that includes the ability to view chromatograms and to use
them in shotgun assembly. Please click here to learn why sequence assembly is easier with a program that
can use chromatograms.

MacVector

This long-lived program was recently updated to allow viewing chromatogram files, plus it runs under
MacOSX - the only complete sequence analysis program of which I am aware. It appears that it cannot
show the raw trace data, however - a distinct deficiency, in my opinion, but a common one for these
chromat viewers.

Programs that can read Genotyping/fragment analysis chromatogram files include:

Peak Scanner from Applied Biosystems, Inc.

This is a FREE program from Applied Biosystems, the company that made our sequencers. I have heard good
things about its capabilities, and some of the Core employees have tried it out, as well as several
of our clients. I have not tried it myself yet.

GeneMarker from SoftGenetics, Inc.

While this program is not free by any means, the UM DNA Sequencing Core has several copies available
for checkout, free for our on-campus Core clients. This program is for the PC only.

DAx from Van Mierlo Software Consultancy.

Many people have reported success using this program in the past, but we have no recent experience
with it. According to its author, this program runs on Windows machines of all sorts, as well as
Mac/Intel and Macs emulating a PC. See the above link for further information.

STRand from the Veterinary Genetics Laboratory at UC-Davis.

I know little about this program. It is open-source, distributed under the GNU General Public License,
which is a marvelous idea. The screenshots look super, the executable download runs on various Windows
machines, and the source code is available (presumably so you can try installing it on other computers).


2. Configure Your Computer So It Recognizes Chromatogram Files

Different computers use different mechanisms to recognize a file's content and to call up the
appropriate software to open it. Not surprisingly, Macs and PCs are quite different in the way
they approach this task. Here's how you tell your computer what to do with files of type '.ab1'.

A Windows system ('PC') recognizes files types by the three-letter extension.

A file ending in '.txt' is expected to contain text, and can be opened with, say, WordPad. A file ending
with '.doc' is more complicated, and should be opened with Microsoft Word. Sequencing chromatograms
should end in '.ab1', and your computer needs to open it with Chromas or ABIView or similar (see
above).
Genotyping (Fragment Analysis) chromatograms end in ".fsa", and should be opened with GeneMarker, DAx,
STRand or similar.

To tell Windows what program to use: download the first chromat file, then double-click it. A window will
pop up telling you it doesn't know how to open the file. It will offer to let you browse for the correct
application. Do so - choose the chromat viewer you downloaded above. Windows should thenceforth remember
what program to use. You can continue to download the rest of your files.

An OS X Macintosh also recognizes files types by the three-letter extension.

A file ending in '.txt' is expected to contain text, and can be opened with, say, TextEdit. A file ending
with '.doc' is more complicated, and should be opened with Microsoft Word. Sequencing chromatograms
should end in '.ab1', and your computer needs to open it with, say, 4Peaks (see above).
Genotyping (Fragment Analysis) chromatograms end in ".fsa", and you MAY be able to open them with DAx,
STRand or similar, but Mac users are more limited here. I have had some success with running GeneMarker
under PC emulators.

To tell an OS X Mac what program to use: download the first chromat file, then single-click it and pull the
'File' menu to 'Get Info (or type command-I). In the resulting window, click the arrow next to 'Open With:',
and in the pop-up menu button underneath, browse for the chromatogram viewer application. You may wish
to click the 'Change All' button, to tell your computer that it should always use that application for 'ab1' files.


3. Access our Data Server to obtain your chromatogram files

If you've completed the above two steps, you should be all set to download all your chromatogram
files. If you get some 'ab1' files and still cannot open them, please review the first two steps, above.

You have two choices for downloading files:

Just a Few Files: Download Them via Web

If you have only a few files, it's easiest to use the login screen in our Download Results page. Identify your PI in the
form and click 'Login'. A password screen will pop up asking for your PI's Login name (again) and your lab password.
Type the PI Login in lower-case, please.
Once you are logged in, click on a lab member's name and you'll get a list of
chromatogram and seq files. Click on any file to download it. If your computer asks you what to do with the file, just
tell it to save the file to disk. You can open the file later using your chromat viewer.

Everyone in the lab should know the lab password! It is required for downloading results
as well as for editing or deleting submited samples!

Lots of Files: Use an FTP Client

Rather than clicking on dozens of files one at a time (as with the web-based download, above, you can get lots of files
quickly using typical FTP clients. Mac users can try Fetch while Windows partisans might try WS-FTP or FileZilla.
Set the host to:
              seqcore.brcf.med.umich.edu
    

Please set your program to use PASSIVE transfers!

Check the instructions that come with your FTP program to find out how to set it for 'passive' connections, how to open
a new connection, how to open folders, how to request files to be transferred. Usually it is possible to request dozens or
even hundreds of files at once. In older FTP clients, this was the 'mget' command, but in newer graphical clients, it may
be as simple as dragging.

NOTE: It is no longer necessary to set the port number to 8721. The 'normal' FTP port should now work.

PLEASE NOTE: Off Campus clients will NOT be able to access the FTP server without special arrangement with
the Core Director, due to our network security methods. Please use the web-based method, if at all possible.
If you find you really must use FTP, please contact me.


Please address any comment, questions, or suggestions to
  Robert H. Lyons (boblyons@umich.edu)