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Kingsford-Group / squid

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
BSD 3-Clause "New" or "Revised" License
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Parameter recommendations for benign tumor types #6

Closed biobenkj closed 6 years ago

biobenkj commented 6 years ago

The software is fantastic and has been very easy to use! I am opening an issue to ask what some parameter recommendations would be for clonal benign tumor types? Specifically, I'm looking at the -r option for normal/tumor cell ratio. I appreciate your time and any insight.

Congm12 commented 6 years ago

I would think benign tumor has less intra-heterogeneity compared to malignant tumor, so each TSV will get concentrated support from tumor cells. I would suggest setting r to be 1 or 2 to ensure precision.

biobenkj commented 6 years ago

Excellent. Thanks!