Discussion of RNA-seq Tumour Purity

[DarioS]

The user guide describes how purity estimation is done for DNA sequencing. But, could a couple of sentences be added that comment on how feasible it is to do with RNA sequencing? It would be interesting to know the purity of the cancer RNA-seq sample to estimate how much the fold changes are being shrunk between tumour and normal because of normal contamination.

[etal]

If the tumor tissue has enough large-scale copy number alterations then it should be possible to infer tumor purity from the import-rna results the same as you would from the DNA-seq pipeline. It depends on your cancer type and stage; might work all right with melanoma, for example. Let me know how it goes...