The bioBakery help forum

Swtiching from uniref90 to uniref 50 with only unclassified reads

Hi there!
I’ve been enjoying HUMAnN a lot so far, I just have one question.

My samples are from the guts of these tropical carrion feeding bees. I realized after running HUMAnN with uniref90 and default parameters that my samples probably are very uncharacterized and that I should have used uniref50.

Is there anyway to get a fastq of only the resulting “unclassified” reads and then run uniref50 on those? Or what do you think is the best way I should go about getting those classified? I have 95-99% unaligned reads after nucleotide and translated alignments. So, I’m just assuming it’s because I didn’t use uniref50 but is there any other reason you image that could be?