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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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Inverting tumour and saliva BAMs in tumor-normal paired gives the same results #7

Closed timothee-revil closed 3 years ago

timothee-revil commented 4 years ago

Hi,

As a quick check for the calls obtained, I ran the analysis in reverse, that is using the tumour as a normal sample, and the normal sample as a tumour. Strangely, this gives exactly the same results as a normal analysis.

Is this expected?

Thanks, Tim

PengJia6 commented 4 years ago

Hi,

As a quick check for the calls obtained, I ran the analysis in reverse, that is using the tumour as a normal sample, and the normal sample as a tumour. Strangely, this gives exactly the same results as a normal analysis.

Is this expected?

Thanks, Tim

Hi Tim,

Thanks for your test! I guess you use msi command. If that, this is expected. msi command in msisensor-pro is same with that in msisensor. msi command just capture the instability singal by comparing the microsatetllite difference between tumor and normal sample using chi-square test. Did I answer your question?

Best, Peng

timothee-revil commented 4 years ago

Yes, this answers my question perfectly. This is a bit what I had guessed.

Thanks again for this tool, works great for what I'm doing!

Tim