Do LoF/GoF (e.g. missense mutation) transcripts count toward the RNA-seq TPM count? Or would these LoF/GoF transcripts only be detected by isoform quantification?
Yes in general missense mutations will rarely affect alignment (unless the gene is already very homologous with other regions - which is rare). Thus they will contribute to counts (and of course TPM).
However, if the missense mutation occurs at a splice junction it could ultimately decrease overall counts for a transcript (or in rare cases increase them).
LoF/GoF are phenotypic descriptors and could include the loss of whole exons or protein domains; in such cases they would affect counts.
thank you. you read my mind about splicing.
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