Question: msi sensor for microsatellite instability detection
gravatar for manasa22.reddy
22 months ago by
United States
manasa22.reddy40 wrote:

Hi everyone ,

I have been working with MSI sensor pipeline, I got the following error - "Same reference genome file should be used in both 'msisensor scan' and 'msisensor msi' steps!!!"

I am working on GSE 30833 dataset and specfically using GSE64988 tumor sample.Used hg18 as reference genome as mentioned in their read me file.

Did anyone use the pipeline before ,please let me know your comments

next-gen • 1.0k views
ADD COMMENTlink written 22 months ago by manasa22.reddy40

Hi, Just make sure the reference genome file(hg18) you have used to create the bam files of your sample data is the same to generate the microsatellites.list(msisensor scan). I have also faced the same issue. Try this. It worked for me.

ADD REPLYlink modified 21 months ago • written 21 months ago by saranseth940
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