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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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What is the cut-off value should I use? #4

Closed jsonProgram closed 4 years ago

jsonProgram commented 4 years ago

hi Jia,

Is it as same as msisensor2? cut-off value =20?

and, for different sample type should have the different cut-off value ?

Json

PengJia6 commented 4 years ago

hi Jia,

Is it as same as msisensor2? cut-off value =20?

and, for different sample type should have the different cut-off value ?

Json

Hi Json,

MSIsensor-pro and MSIsensor2 are two different software for MSI calling. In MSIsensor-pro, we did not provide a cut-off, because the cut-off will be different for different sequencing panel. If you want to use MSIsensor-pro in a new panel for only tumor sample MSI detection, please use the msi status from msisensor or gold standard as true value to obtain a cut-off suit for your panel.

By the way, it seems that MSI is a continuous value, and you can just use msi score for you research.

Best,

Peng