What Is The Difference Between Genome Reference And Transcriptome Reference?

Question

[swilsonn86]

Hi,

I wanted to know about the difference between the genome reference and transcriptome reference. Are there any packages which only use one of them? And is it a way to generate a transcriptome reference from a genome reference?

Thank you for your help BR

[Josh Herr]

I would echo Chris's answer below. What do you mean by packages that only use one of them? Can you clarify your question? You could generate regions with ORFs or predict gene models from a genome reference, but it's not precisely a transcriptome reference. You didn't give us much info on for your research question so it's hard to suggest you could use one or the another.

Answer 1

[Chris Miller]

Transcriptome references generally consist of only the coding regions of the genome. This may include genes with all of their introns spliced out, as well as all known transcripts of a gene, including alternate starts or splice junctions, exon skipping, etc.

[swilsonn86]

Thank you and is it possible to generate a transcriptome reference file from a genome reference file?

[Arun]

If you have a gene model (a GFF or GTF file with known genes and isoforms), then its just a matter of putting together the sequences from the genome (fasta) for each gene taking their transcript coordinates, I'd think so. In case a gene has multiple isoforms, I wonder how one would go about? I'd suppose merging the isoforms to obtain a on-the-whole-representation of the gene would make sense... (in other words, the longest possible sequence where every isoform is a subset of this constructed sequence)?