I would like to analyze my RNAseq profiles from bulk tissue samples (Paired-End, 50M reads/sample, tumour-normal pairs) with varscan2 to detect mutations.

Then I would like to use those detected mutations to estimate presence of different tumour clones (likewise pyclone on WGS data). Therefore my questions:

  1. Is it possible to estimate number of clones and clonal abundancy from RNA seq profiles from bulk tissue? and if yes: are 50M reads/sample enough coverage.

  2. Could you recommend which package to use for this, for example is pyclone suitable for this?

Thank you in advance for the advice!

  • $\begingroup$ I guess this is not possible, as mutation frequencies (ratio of reads with and without mutation) used in this cluster approach depend highly on transcriptional regulation in the different clones, and does not only depend on the presence or absence of the mutation. $\endgroup$ Oct 23 '18 at 11:17

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