Do LoF/GoF count toward transcript count?

Question

[Kermit]

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?

Answer 1

[benformatics]

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.

[Kermit]

thank you. you read my mind about splicing.