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niu-lab / msisensor2

Microsatellite instability (MSI) detection for tumor only data.
GNU General Public License v3.0
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Issues about the cfDNA result #12

Closed jsonProgram closed 4 years ago

jsonProgram commented 4 years ago

hello Dr.Niu, I had test MSIsensor2 for cfDNA sample.

There is some issues confused me.

At First I try the Tumor-Only for the cfDNA sample:

<<# CODE START bin/msisensor2/msisensor2 msi \ -d hg19.list \ -t cfDNA.bam \ -o output/Tumor-Only \ <<# CODE END

hg19.list : bin/msisensor2/msisensor2 scan hg19.fa -l 7 -o ./hg19.list

<<# Result Total_Number_of_Sites Number_of_Somatic_Sites % cfDNA-sample-1 2456 219 8.92

And then I get the PBMC sample for this cfDNA from the same blood tube. <<# CODE START bin/msisensor2/msisensor2 msi \ -d hg19.list \ -n PBMC.bam \ -t cfDNA.bam \ -o output/Tumor-Only \ <<# CODE END

<<# Result Total_Number_of_Sites Number_of_Somatic_Sites % cfDNA-sample-1 2275 495 21.7

This result is confused me. Any suggestion?

ps:PBMC and cfDNA uses the WES Panel and NGS sequencing.

Json

owehann commented 4 years ago

Hi Json For tumor only method , -M paramter must be specified, and I think, the models_hg19_GRch37 is suitable for your bam. Actually, we have a beta version with advanced algorithm which has already shown its powerful classification ability on our cfDNA samples. Leave your email and we can offer it to you. Simultaneously, as the first users trying our new method, we hope you can provide detailed information about your cfDNA samples and final results. Besides，if your are willing to provide your samples, we can have a more in-depth cooperation. Thanks Xinyin

jsonProgram commented 4 years ago

Thank for your Help!

Json