[Automated-sequencing] Fragment analysis--GeneScan Analysis problem

Stewart, Amanda via autoseq%40net.bio.net (by AStewart from bethanywv.edu)
Thu Aug 6 07:30:39 EST 2009


I am returning a refurb ABI 310 to use, primarly for fragment analysis using GeneScan.


No matter what I try, I can't get GeneScan to analyze any peaks past 200 base pairs.  If I try to analize with ANY size standard file that is longer than 200 bp the analysis fails.

I've made my own size standard file from Rox500 standard, I've used the default size standards--and the ONLY ones that work are one I made that goes to 200bp (using Rox500 size standard sample to make the file) and the default one on GeneScan that is 120bp.

When I look @ the raw data or the data analyzed with my 200bp size std or the 120 bp size standard, the Rox 500 size standard peaks are there & are just perfect---but it won't size call them and if I try to use any other size standard file it just fails the analysis.

I've even made different analysis parameter files--all of these will work/analize with the two "small" size standard files...but nothing works if I try a size standard bigger than 200.

WHAT TO TRY NEXT?

I also can't get the collection software to start GeneScan and autoanalyze, even though I've told it to in both pieces of software (both GeneScan and Collection should "know" to do this...sigh.) I canlive with this one...no problem to analyze later, but I really need to figure out why I can't size peaks past 200 bp.



Any suggestions would be GREATLY appreciated!







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