MSIsensor parameters

Jane M · 08-21-2017, 07:53 AM

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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08-21-2017, 07:53 AM	#1
Jane M Senior Member Location: Paris Join Date: Aug 2011 Posts: 239	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