Is a "transcript annotation" different from a "genome annotation?"

Question

[yh1126]

By what I understand, genome annotation is an information of where all the genes are on the reference genome sequence. Is a "transcript annotation" different?

It logically seems that a genome annotation file is sufficient to provide information on which genes all the transcript reads came from (and that is usually all is needed in a typical RNA-Seq analysis), and I've never heard of a separate annotation for transcripts that is different than one for the whole genome.

When a program asks for a transcript annotation, can I just give the genome annotation file from NCBI (GFF or GTF format)?

In the same vein, is a "reference transcript" different from a "reference genome?"

Answer 1

[Emily]

1. Genome annotation and transcript annotation mean pretty much the same thing: marking the position of transcripts on the genome.
2. The reference genome and reference transcript mean very different things. The reference genome is the whole genome that we align reads to, for humans this is 6GB of sequence, 24 chromosomes and a mitochrondria. A reference transcript is just one of the thousands of transcripts mapped to that sequence, a few thousand based, spliced.