kharchenkolab / numbat

Haplotype-aware CNV analysis from single-cell RNA-seq
https://kharchenkolab.github.io/numbat/
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Experimental Data Expectation is Unclear #154

Open DarioS opened 4 months ago

DarioS commented 4 months ago

The journal article uses purified cancer cells (and does not state what flow cytometry markers were used for sorting by).

... with sample-matched, flow-sorted WGS.

The software user manual mentions bulk whole genome sequencing may be input.

Sometimes users already have CNV calls from bulk WGS, WES, or array analysis.

How low can tumour purity be before it harms, not helps, statistical inference? Some clarifying sentences in user guide are needed.

teng-gao commented 4 months ago

Thanks, we'll consider adding some more instructions on this.

The journal article uses purified cancer cells (and does not state what flow cytometry markers were used for sorting by).

These info should be in the original Liu et al paper where the data was first published.