Allele Call FAQs

allele_call: Frequently-asked questions

I have changed the "Min_size_standard" and "Max_size_standard" in
"settings", but "allele_call" is not re-analyzing the gel.
[4/21/97]

The default settings for your "Redo"s are "no". To force allele_call to re-analyze the gel, you must do either of the following:

Turn the appropriate "Redo" settings on. For example, in your case, you want "allele_call" to re-construct the manifold, so you would set "Redo_manifold" to "yes" before you invoke allele_call; or
Directly call the corresponding program. In your case, you would call image_call to reconstruct the manifold, and then followed by allele_call to re-genotype.

I'd like to re-analyze a gel from scratch.  How do I do that?
[4/21/97]

You can invoke "reset_now gel " to delete all the previously computed results.

I added a third gel (GEL3) to my study, which contained 2 gels (GEL1
and GEL2) that I have analyzed before.  I called "allele_call" on the
study, but I aborted it before completion.

Now, when I call "allele_view" on the study or on GEL1, it says "GEL1
has not been genotyped".  But I have genotyped GEL1 before!  What
happened? 
[4/21/97]

Every time you call "allele_call" on a study or a gel, it marks all the gels involved as gels that are to be genotyped, regardless of whether the gel has been genotyped before, or whether the "Redo_quantitate" and "Redo_allele_call" settings are turned off.

When your "allele_call" session was aborted pre-maturedly, these gels are left in an inconsistent state, and you should not call "allele_view" on the study or any of its gels, as "allele_view" ASSUMES that "allele_call" has been run to completion.

If you want to "allele_view" GEL1 and GEL2 again without re-quantitating and re-genotyping the gels, you can call "allele_call" on these gels by setting all the "Redo_*" settings to "no". Let "allele_call" run to completion on these gels and you can view the genotypes using "allele_view" again.

In the meantime, you should take GEL3 out of the study and analyze it individually first. You can always add it back to the study for "allele_view" across multiple gels later.

Back to FAST-MAP