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seasoncloud / Clonalscope

Clonalscope is a subclone detection method based on copy number alterations (CNAs) for single-cell and ST tumor sequencing data. Clonalscope is able to detect subclones, label malignant cells, and trace subclones for both scRNA-seq and ST data.
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Tutorials Lack Details About Handling Low Tumour Purity Samples #4

Open DarioS opened 1 year ago

DarioS commented 1 year ago

It looks like the method was evaluated only on samples with high tumour purity.

All epithelial cells in the metastasized tumor P6198 are malignant cells. The three primary tumors (P5847, P5931, and P8823) have high purity and thus most of the epithelial cells are expected to be malignant.

The tutorials should explain what to do if estimated purity is 30% to 50% from whole genome sequencing by e.g. PURPLE.

jiazhen-rong commented 1 year ago

Hello @DarioS , thank you for the suggestion. Currently we are working on the mode without paired WGS, as shown in the side branch tutorial 4, which could be an alternative option for when WGS purity is low.