Can I readmap short reads to rDNA references?

Question

[aniigodwinn]

I have some reads that I want to assemble but there is no genome available for this species that I can find. Can I perform the read mapping to a rDNA references or how can I go about it?

[GenoMax]

I have some reads that I want to assemble but there is no genome available for this species

You don't need a genome for assembling reads. As long as the reads are from just one organism you can simply try to assemble them.

If you are interested in identifying rDNA reads in the data you could align against a close relative or use a tool like ribodector (LINK).

[aniigodwinn]

Thank you! I will try this now.