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  • 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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