Question: What Is The Difference Between Genome Reference And Transcriptome Reference?
2
gravatar for swilsonn86
6.3 years ago by
swilsonn8620
swilsonn8620 wrote:

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

genome reference transcriptome • 4.7k views
ADD COMMENTlink written 6.3 years ago by swilsonn8620

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.

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Josh Herr5.6k
1
gravatar for Chris Miller
6.3 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

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.

ADD COMMENTlink written 6.3 years ago by Chris Miller20k

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

ADD REPLYlink written 6.3 years ago by swilsonn8620

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)?

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Arun2.3k
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