TTE gels

Glenis Wiebe gwiebe at ucalgary.ca
Tue Aug 1 10:00:08 EST 2000


Hi Michelle,

I'm not surprised to hear that changing the basecaller made a big difference.  I
know that some TTE protocols call for the ABI50 or SemiAdaptive basecaller, but we
find that the ABI LongRead basecaller (LR-377) works much, much better.  We found
the others require too much hands on adjusting (changing the start point, the
spacing, etc.).

Glenis


Biopolymer Facility wrote:

> Hi Glenis,
> To answer your previous question:
>
> >No, we haven't had this problem (knock on wood).  I presume you are seeing
> this with your controls as well?
>
> Yes, it was present in all the samples on that gel, in varying degrees -
> some samples looked better than others. One suggestion that was made to me
> was to use the ABI LongRead basecaller. I reanalyzed with that and while
> that early region was still not great to look at, the basecalling was
> fairly significantly improved. I think my next step is going to be to
> remake that buffer - I did have a student make it up so one only knows.
> Thanks for the input...
>
> Michelle
>
>
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> Biopolymer Facility
> Roswell Park Cancer Institute
> Buffalo, NY   14263
> Phone: (716) 845-8032
> Fax: (716) 845-7621
> Email: biopolymer at sc3101.med.buffalo.edu
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