Is there a way to combine dna and rna reads?

Question

[Mageiros]

Hi.

I am working on a project that has metagenomic and metatranscrptomic samples from patients. Some of these samples where taken at the same time point from the same patients.

At the moment I am analyzing separately the metagenomes and the metatranscriptomes, running two distinct differential expression analysis pipelines.

I was wondering if there is a "smart" way to combine the metagenomic and metatrascriptomic reads that are from the same patient and the same time point so I can run one unified analysis on both types of samples?

Looking a bit online, I couldn't find anything but I thought I could ask either way.

Note that my DNA and RNA libraries were created independently.

Thx a lot in advance.

Best Leonardos

[iraun]

I think the first is to be sure of "why" you want to combine RNA and DNA reads, since these two data types offer different kind of information. Second, usually tools work either with RNA or DNA, or if they work with both, the tools prefer if you only give as input RNA or DNA and set up the tool parameters accordingly. Maybe the most sensible is to use both datasets independently, and verify if the results are concordant, unless there is a tool that does what you need that takes as input both RNA and DNA-Seq reads (I am not a metagenomics expert, so I can't help here).

Answer 1

[Asaf]

I too couldn't find a proper way to analyze metatranscriptomics data. The best way would be to generate an assembly, map the RNA to the metagenome and analyze each MAG or scaffold individually. However, this will require very deep sequencing and will be effective for the highly abundant bacteria.