FAST-MAP Protocol FAQs

Typical protocol for FAST-MAP: Frequently-asked questions

What are the operating procedures that you would recommend for using
FAST-MAP regularly?

[6/12/97]

FAST-MAP is a fully-automated genotyping system. On good gel data, calling just "allele_call <study>" is sufficient. In fact, that was all we did for the demo gels that we have provided with the FAST-MAP software.

However, we may not always get perfect data in day-to-day use. It may turn out to be more effective to break down the single-step genotyping process to smaller steps so that we (the user) can ensure the quality of the partial results before we proceed further. FAST-MAP has been designed with various checkpoints for the user to interact with the data.

The following is a recommended protocol for FAST-MAP users who have to deal with real data regularly:

STEP 1: Setting up the study
Define the "markers", "panels" and "size_stds" (if necessary), then use the "setup" program to set up a study and its component gels:
```
        >> edit markers
        >> edit panels
        >> edit size_stds
        >> setup study
```
If you should encounter problems during "setup study", just fix the problems indicated by "setup", and then call "setup study" again until you have successfully set up the study and its component gels.
STEP 2: Converting gel images into FAST-MAP format
Since FAST-MAP is sequencer-independent, we need to convert the sequencer-specific gel images into FAST-MAP format before we can view the images in FAST-MAP:
```
          >> prep_call <study>
```
STEP 3: insecpting the dye-separated images
In this step, we inspect each gel's dye-separated images:
```
          >> prep_view <study>
```
In particular, we do the following:
- Set the "Star Scan" to trim away any primer gel regions, and if necessary, also set the "End Scan" to trim away any excess unused gel region on the other end;
- Take note of any unloaded gel lanes, and "edit <gel> layout" to correct if necessary; and
- Take note of the smallest and biggest detectable size standard, then "edit <gel> settings" to set the "Min_size_std" and "Max_size_std" for that gel.
STEP 4: tracking lanes automatically
You are now ready to try the automatic lane tracking and MW size calibration:
```
         >> image_call_STU <study>
```
Or, if you prefer to do it gel by gel:
```
         >> image_call_GEL <gel>
```
If you have many gels in the study, you may want to take a coffee break now (allow at least 10 min per gel).
Please see useful debugging tricks and generating bug reports for an explanation on using the specialized "image_call_STU" versus "image_call".
STEP 5: inspect the sizing grid
Inspect the sizing grid and repair any misplaced peaks if necessary:
```
         >> image_view <study>
```
STEP 6: determine marker windows (optional)
This step is strongly recommended for every new panel that you use. Typically, view the marker windows over 2-3 gels (more if you want) and set the correct allele window with "Start BP" and "End BP":
```
         >> marker_view <study>
```
STEP 7: calling the alleles automtically
This is the computation-intensive step. You are free to leave the computer for a couple of hours and return to view the results later.
For a study:
```
   >> allele_call_STU <study>
```
For a gel:
```
   >> allele_call_GEL <gel>
```
You can also use "allele_call" without the "_STU" or "_GEL" extension if you prefer. See useful debugging tricks and generating bug reports.
STEP 8: viewing and editing the genotypes You can peruse and edit the genotyping results with:
```
	>> allele_view <study>
```

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