Does MSIsensor or MSIsensor2 work with tumor-only RNAseq data?

[audyavar]

Hello @Beifang -

I am an avid fan of MSIsensor and routinely use it in the calling of MSI status from exome sequencing data. Recently we have started to switch our analysis to RNAseq data and I was wondering if MSIsensor(1 or 2) works on tumor-only RNaseq data? Another question for you is if it works on mouse data (exome/rnaseq) as well?

[Beifang]

Thanks for your interest on msisensor suite. We have not test on RNAseq data. msisensor should works for mouse normal-tumor paired exome data and for msisensor2, we currently have no enough wes/RNAseq data to train tumor-only models for mouse.

[audyavar]

We have quite a few samples to run this on human RNAseq data. Any advice on changing any parameters for applying MSISENSOR on RNAseq data?

Best

Akshata

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From: Beifang Niu notifications@github.com Sent: Tuesday, November 5, 2019 6:34 PM To: niu-lab/msisensor2 Cc: abio; Author Subject: Re: [niu-lab/msisensor2] Does MSIsensor or MSIsensor2 work with tumor-only RNAseq data? (#6)

Thanks for your interest on msisensor suite. We have not test on RNAseq data. msisensor should works for mouse normal-tumor paired exome data and for msisensor2, we currently have no enough wes/RNAseq data to train tumor-only models for mouse.

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[Beifang]

please just try: msisensor2 msi -M ./models_hg19 -t rnaseq.bam -o xxx.prefix to see what would happen.

[courcelm]

@audyavar Any success with RNAseq data?