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Update Practical 3b Processing 16S rRNA reads extracted from PacBio long reads authored by Taylor Priest's avatar Taylor Priest
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## Extracting 16S rRNA gene sequences from long PacBio reads
If, instead of amplicon sequencing, you performed metagenomic sequencing (whole community DNA) then you can still assess community composition using phylogenetic marker genes such as the 16S rRNA gene. In order to do this, however, you need to extract the marker gene sequences from the long reads.
The best tool for performing such an action is **Barrnap**. Check out the github repository of this tool to understand more: https://github.com/tseemann/barrnap
In short, Barrnap using hidden markov model profiles of known 16S rRNA gene sequences to search for those in your data.
The command to run Barrnap is as follows:
$ barrnap --kingdom bac --threads 10 input_seqs.fa --outseq output_seqs.fa
Great, once you have your 16S rRNA gene sequences, we can then analyse them using DADA2.
## DADA2 ## DADA2
Before we begin using DADA2, we need to tell our bash profile which version of R we want to use. Thankfully, the IT department previously set up a specific version of R that already has DADA2 and most of the necessary dependencies already installed, which saves us a lot of time. Run the following lines of code to direct your profile to the correct version of R and then start Rstudio: Before we begin using DADA2, we need to tell our bash profile which version of R we want to use. Thankfully, the IT department previously set up a specific version of R that already has DADA2 and most of the necessary dependencies already installed, which saves us a lot of time. Run the following lines of code to direct your profile to the correct version of R and then start Rstudio:
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