What is the standard input for gene expression for pVACtools?

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What is the standard input for gene expression for pVACtools? #1032

Closed PierreLaplante closed 8 months ago

PierreLaplante commented 11 months ago

Hello,

My pipeline uses HTseq-counts for quantifying expression of genes. How should I normalize the raw count table output of HTseq-counts for annotating the .vcfs to be usable with pVACtools?

Thank you.

susannasiebert commented 11 months ago

There are a few different measures for gene/transcript expression. In our pipeline we use Kallisto, which I believe outputs TPM abundance values.

susannasiebert commented 8 months ago

Closing this issue due to inactivity.