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.

[aniigodwinn]

Still on this, the reads are from org a, org b, and environmental contaminants. I have a fairly good idea what org b might be but i need to be able to show this on a rDNA tree. I also have the 18s rDNA seequences from NCBI of org b.

My problem is going from the reads which contain many orgs to a rDNA tree showing org b is one of the many orgs.

[GenoMax]

If these are short reads and the organisms are related then you are going to have a difficult time classifying the reads.