How to do RNA-seq assembly to a reference genome for the first time?

Question

[yomirann]

Hi all, I want to do total RNA-seq and to perform the assembly to the reference genome of that species for the first time. I have RNA-seq from related species. What tools do you recommend to work with? Any help will be much appreciated.

Thanks!

[h.mon]

Your question is not clear. From what I understand, you have a reference genome, but the RNAseq is from a closely related species, is this correct? If so, you can map the RNAseq reads to the reference genome with STAR, HISAT2 or some other splice-aware aligner, and then use StringTie to assemble the transcriptome.

You may also consider performing a de novo assembly, as mapping rate, and hence final assembly, will be bad if the reference genome is not from a closely related species.

[yomirann]

Hi!

So, I have a fully sequenced high-quality genome. I don't have an RNA-seq for this species. I have RNA-seq for a closely related species. I want to perform total RNA-seq for my species of interest.

What is the best approach? Thanks!