Is dog (Canis familiaris) transcriptome considered well-annotated?

Question

[CandiceChuDVM]

Hi all,

I am thinking whether or not to apply dog transcriptome annotation in the optional transcriptome alignment of TopHat2. I don't think it would hurt unless the quality of transcriptome annotation is really bad and gives us wrong information. I am new in the RNA-seq research. From my point of view, it looks like only human and mouse transcriptomes are considered well-annotated (or maybe I am wrong).

How about your opnion on the dog transcriptome (Canis familiaris)? Would it hurt to apply it in the TopHat2?

[GenoMax]

Simple answer is no. As you suspect the annotation is not going to be as good as human/mouse. In addition you may be working with a breed that may be different (to varying extent) than the reference (a female boxer). But you can run TopHat with and without annotation to compare.
Actually if you are just starting then you may want to switch to HISAT2 instead of TopHat2.

[CandiceChuDVM]

Thanks! I work with labs. I am not sure if labs and boxers are relatively similar in terms of dog breeds but I haven't checked it yet. And yes, I am going to use HISAT2. I was literally reading the HISAT paper when I saw your reply :)

Answer 1

[Chris Cole]

No it won't be. However, for any gene expression (which is what I'm assuming you're using RNA-seq for) study you need a reference annotation to work with. Either at the TopHat stage or when quantifying expression with featureCounts, htseq-count, cufflinks, etc. At best you're going to have to work with what is available which will be incomplete and incorrect in places.

I would also recommend against TopHat. We typically use STAR, but HISAT looks good too.