Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
stringtie parameters sbcn Bioinformatics 6 02-07-2017 07:46 PM
MEME parameters gene_x Bioinformatics 2 04-11-2013 06:07 PM
lastz parameters Vasilis General 0 12-17-2012 01:00 AM
Bowtie parameters khb Bioinformatics 11 12-16-2010 09:08 PM
miRDeep -v and -z parameters NicoBxl Bioinformatics 1 10-04-2010 06:37 AM

Thread Tools
Old 08-21-2017, 06:53 AM   #1
Jane M
Senior Member
Location: Paris

Join Date: Aug 2011
Posts: 239
Question 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
Jane M is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 07:15 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO