I have raw paired-end reads (not yet aligned) that may be bacteria/archaea but could also be eukaryote. I would like to determine their small ribosomal subunit rRNAs in the sample and then compare it to SSU tree that comprehensively spans prokaryotes/eukaryotes/etc. I have basic command line skills.
I am thinking of using RNAmmer or Barrnap just because their vignettes are on the shorter side and make me feel like I can accomplish this analysis a bit more time-sensitive manner for preliminary results. I am having difficulty figuring out a simple pipeline to accomplish this task for two reasons:
1) I am unsure if some of the software (like RNAmmer and Barrnap) can take as input raw paired-end .fastq files. And if not, how to prepare an appropriate input in a straight-forward fashion.
2) How to take the output from RNAmmer and Barrnap (which I believe will tell me the SSU in my sample) and then compare it to comprehensive SSU tree to get a better idea of where my sample fits phylogenetically with other organisms.
Any advice would be so very helpful.