Hi all,
I'd like to create an annotated genome for a small eukaryotic organism. Ultimately, it will be used to conduct a transcriptomic analysis using illumina paired-end RNA-seq data that I obtained previously. There are no sequenced genes for the species, but there are sequenced genomes/genes for other members of the genus (it's a very small genus). The reason we've decided to annotate the genome is that this species is the most distantly related.
Would I still able to blast genes from other species within the genus? Or would a genome annotation be possible at all? I know that de novo assembly is an option, but I was hoping for a genome annotation over de novo if possible
Any advice is welcome regarding where to begin/which softwares/packages etc.
If the species are closely related then you would indeed be able to align your data to the available reference. It can also help you identify how complete your own sequence may be (if the reference genome is well finished). And then there are ways of doing reference guided genome assembly.
The reference genome is quite good, as there weren't many genomic repetitive regions. The genome is about 380 Mbp. Do you know what the best way to complete this would be? Again, thank you in advance for any advice you can provide
I suggest starting with
STARorbbmap(splice aware aligners). Alignment % would likely vary but should be pretty high for a related species. Once you align your data you can visualize it using IGV. That would give you an idea of what the data looks like. Use RSeQC to evaluate the alignments.In parallel, you can also use Trinity to assemble your data into a transcriptome and then compare it to the one from known reference.
Note: Since you have RNAseq data you can't really create a genome for your species as you said in title of this thread. You are restricted to constructing/evaluating the transcriptome.