Estimate microbial diversity with rRNA

[Shicheng-Guo]

Dear Sam,

I remember, in metagenome research, we can use 16S rRNA to estimate metagenome diversity. I am thinking why it is not showed in the samsa2 pipeline since in the default mode, samsa2 remove all rRNAs.

Thanks.

Shicheng

• The flag --num_alignments 0 in the ribosomal sortmrna step has been removed. This caused problems and slowed things down a lot. Plus, we don't care about the rRNA alignments - whether a sequence aligns to 1 or 1,000 rRNA, it's out anyways...

[transcript]

Hi Shicheng,

One issue with including the 16S rRNA is that it is only able to provide a limited resolution for metagenome organism identification. With this pipeline, the goal is to identify down to genus and/or species level resolution, which is where 16S rRNA struggles.

Another challenge is that, if an individual is doing metatranscriptome research, they're likely going to run a depletion step in their wet-lab protocol. rRNA depletions don't equally target all 16S sequences, and so the 16S results will be skewed by that step.

For this reason, the SortMeRNA step removes rRNA sequences by default. You are always free to customize the pipeline to leave it out and include rRNA results, if you prefer, but it is unlikely to provide additional information when it comes to the metatranscriptome activity profiles.

Best, Sam