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Jane M 08-21-2017 06:53 AM

MSIsensor parameters
 
Dear all,

I am using MSIsensor for the first time.
As a first test, I launched it on my paired (realigned, recalibrated) bam files using default parameters and got the output files without problem.
I was a bit surprised because I expected a high score for MSI for some samples, while it was ~3.7 only for 2 samples.
So now, I would like to clearly understand and refine, if needed, the parameters, knowing that I am working with human samples.

msisensor scan
  • context length -c 5
    What does it represent?
  • minimal/maximal homopolymer size -l 5 / -m 50
    Nb of bases forming a repeat unit, between 5-50
  • maximal length of microsatellite -s 5
    I am not sure: is it the maximal number of bases forming a repeat unit in a microsatellite. Isn't it small?
  • minimal repeat times of microsatellite -r 3
    Minimal number of repetitions to form a microsatellite

msisensor msi
  • minimal homopolymer size -l 5 / -p 10
    Why changing the threshold for distribution analysis?
  • minimal microsatellites size -q 3
    Is it equivalent to -r in scan mode?
    Again, why changing the threshold for distribution analysis with -s 5?
  • maximal microsatellites size -w 40
    There was no threshold for that in scan mode. Why this difference?

Does what I understood seem correct and could you give me some clues about the parameters I did not catch?
Thank you in advance for your help


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