read count distribution

[Jemkon]

Hello,

I am new to MSI analysis. I would like to get the length of the microsatellite and the number of reads. Can I get this information from MSI output?

The MSI_dis file contains counts but I dont know whether I should sum all counts to get read count for that sample. Also how to get the length of the microsatellite?

Many thanks,

[ZhaoDanOnGitHub]

Hi,
You can get the length of the microsatellite from microsatellites.list by repeat_unit_length multiply repeat_times. Note, there is another way to get it from MSI_germline or MSI_somatic by repeat_times multiply the length of repeat_unit_bases. The sum of couts per sites is the number of reads for this sites.
Thanks,

[Jemkon]

Hi,
I have extracted it from MSI_somatic files. Many thanks.