I had some troubles with this as well, I did a quick fix by creating a new ROX scale by excluding both the 35 and 50 lengths markers (ROX500, -35,-50). This eliminated confusion on Genemapper's part by throwing out all the data below 50 and making the remaining data much clearer. If you look at the Raw data and you see a lot of peaks in the area before the 50 marker, then this should help - if not I do not have a fix. Hope this helps.

I had some troubles with this as well, I did a quick fix by creating a new ROX scale by excluding both the 35 and 50 lengths markers (ROX500, -35,-50). This eliminated confusion on Genemapper's part by throwing out all the data below 50 and making the remaining data much clearer. If you look at the Raw data and you see a lot of peaks in the area before the 50 marker, then this should help - if not I do not have a fix. Hope this helps.

As Paul said, throw out the short sizer peaks that are muddled by noise (typically 35 and 50) from your sizer definition (in Genemapper Manager menu, I think). Also, Genemapper will frequently mess-up sizer calls, especially if you have pull-up into orange (or red for ROX users) from too strong peaks in other dyes. You can manually call sizing peaks for each sample in genemapper by right-clicking them in sizer view (I don't have a genemapper installation at hand to check which specific button you need to press - you can look at only the sizing info/electropherogram for each sample). When you're satisfied with sizer calls just re-analyze the sample and voila!, your sample should be genotyped. :)  Anyway, it's good practice to manually check sizing, especially for the samples that get a "yellow triangle" in sizing quality - Genemapper occasionally gets these wrong. 

In any case, write if you have problems finding the sizing view in Genemapper and I'll check exactly which button to press.

Thanks very much to both of you!  Your responses are much appreciated. I'll follow up on how it goes with Genemapper.

I also think manuel removing the short marker peaks, which may mess up with the primer noise peaks, often helps. However, I'm not sure how this influences the microsatellite size calling. Any experience?

This may seem pretty obvious, but, in my experience, Genemapper is a little tricky so, first of all, I would check if the bin set you are actually using is the right one: > Analysis > Analysis Method Editor > Allele > Bin Set. The Bin Set is stored from the previous analysis.

If this is OK, then, as Paul and Thomas said, you can define your own own standard pikes: > Analysis > Size Match Editor > zoom on the X axis and right click on each of the pikes, there you can Delete or Change individually.

I usually use LIZ 500 without the 250 peak but using all other peaks. The error no sizing data means that the software was unable to run the samples and find the size standard.  I don't know why it happens... :)

the above response are correct however sometimes when your samples are highly saturated sizing normally becomes a problem. Either you add more size standard or reduce the amount of samples you mix with hi-di. This has one time happened to me but I resolved it by reducing the. Pcr samples to less than zero point five

Maria, see the product insert for LIZ500. The 250 peak is sensitive to minor variations in temperature. The recommendation is to not use this peak when defining the size standard (for particular softwares, anyway). Similar problems can occur with the 340 peak. This appears to be limited to capillary machines, but who uses 377s and such any more? 

As to Stephen, this also happened to me, not far than last November. It sounds that PCR products were not good. So, proceed by elimination, and try some basic operations: First of all, make sure your DNA is of good quality (make new dosages and new dilutions if needed). Then, (as we did), try to run new PCR, with 1.5 more DNA than usual, and 0.5 less primers. Verify your PCR program and ajust the annealing temperature to 60°C for instance. When making your HiDi mix, make sure you have PCR products in the wells (if you use 1ul). For me, it make sens to have more PCR product and less HiDi, as the size standard is correctly shown on Genemapper. I hope it will help!