Does MSIsensor or MSIsensor2 work with tumor-only RNAseq data?
Opened this issue · 4 comments
audyavar commented
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 commented
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 commented
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 commented
please just try: msisensor2 msi -M ./models_hg19 -t rnaseq.bam -o xxx.prefix
to see what would happen.