Question about using barrnap on reads about barrnap HOT 4 CLOSED

I don't think this is the right tool if you want to scan reads directly.

i think --reject means it won't be in the GFF file output, and --lencutoff is to still keep it but label it as partial. You would need to bring those down dramatically yes. 16S is ~1542 bp long, so 0.1 might work. Or just set them to zero (0).

You could just take the HMM Model files from the db folder and run hmmer yourself?
Maybe even bwa/minimap2 first to bait all the reads against a DB of rRNA genes, then assemble those, or scan those directly.

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Thanks for the suggestions here! I realized that I was initially supposed to identify ribosomal proteins instead of rRNA. Had some trouble using phylosift with some weird dependency issues so I thought this would have been a good alternative but they do two different things. In the future, I'll definitely continue to use barrnap for identifying rRNA sequences.

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Ah ... yes there are 20-30 ribosomal proteins. They are quite conserved and easy to find in assemblies. Good luck.

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@tseemann what would you recommend as "relaxed" and "strict" settings in pulling out rRNA from metagenome-assembled genomes (MAG)?

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