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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
msisensor msi
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
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