More GelReader

Anthony Tomlinson anthony at pplros.demon.co.uk
Tue Jul 26 09:33:32 EST 1994


Previously:
>Anthony Tomlinson  <anthony at pplros.demon.co.uk> wrote:
>>I am interested in any software for the Mac that can calibrate
>>gels/autorads so that molecular weights are calculated from band
>>mobilities using MW markers present on the image.  This is so that I can
>>eliminate my own incompetence with a ruler from data I am collecting
from
>>repeated reprobings of a single Southern blot.  Somebody out there is
>>going to reply: "Use GelReader!" to which I reply "How?!"  I can't get
it
>>to work, even when I follow the instructions to the letter.  Generating
>>the template seems to be the problem; if anyone has specific tips on
>>that, I'll be eternally grateful.
>>
>>Anthony Tomlinson.
>
Carlisle Landel replied:
>Somebody in my lab found a message in bionet.software from
>mangalam at SALK-SC2.SDSC.EDU (Harry Mangalam) describing bugs
>in GelReader.  Basically, the trick is that you *must* have 
>a lane of standards on each side of your samples for the thing
>to work.
>
>I've tried using it, and it is still a bit buggy, mostly in that
>I have a hard time getting it to see all my bands:  if there are
>a bunch of small faint bands, upping the sensitivity of the image
>capture program causes the bright large bands to run together, so
>that the program can't differentiate them, while not doing so
>causes it to miss the faint ones.  Also, if you have bands that
>are close together (eg the top of a 1 kb ladder), it seem to want
>to assign differing numbers of bands to the ladder each time it looks
>at it, which is definitely a pain when you are setting up your file
>of size markers.
>
>So I was wondering, does anybody know of a program out there that will
>take manually entered restriction fragment size data and assemble it
>into a map for you?  I'm busy slogging through some mapping of
>some cosmids, and since GelReader isn't working for me (too many bugs
>in my hands) I thought I'd try something else.

Thanks for the tip.  It works, but what use is it?  I have autorads with
some 8 sample lanes flanked by two marker lanes.  There is no way I can
run marker-sample-marker, and to past marker lanes around sample lane
images is hardly less arduous.  Can anyone think of a way to use the
multiplexing function to get around the problem (or doesn't that work
either?)?

On the subject of bands, I have given up entirely on the Find Bands
function;  I just assign bands manually using the + and - tools.  Sorry,
but I don't know of any programs that will generate your maps for you.

I'm going to e-mail the authors direct, but if they or anyone else out
there has any information on revisions etc, or ANYTHING which will
improve GelReader, please post!

Thanks,

Anthony Tomlinson.



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