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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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A few questions about baseline making #52

Open RADIOMUMM opened 1 year ago

RADIOMUMM commented 1 year ago

HI ！ I'm a little confused about baseline making！ 1.Where do the BAM files needed to create Baseline come from? 2.Does the data have to come from the sample itself? 3.As long as the reference uses the same, it can be used as a normal bam for baseline?

Best jennis

PengJia6 commented 1 year ago
  1. Samples from the same sequencing solution, maybe from the same panels. It depends on your application. 
  2. If you have both tumor and normal samples from an individual, you can use the msisensor msi. 
  3. The baseline is used to filter out the bias caused by the sequencing platform, wet lab excrement, genetic background, etc.