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  • locon833
    Junior Member
    • Aug 2014
    • 3
    #1

    Filtering Specific OTUs in Phyloseq to BLAST sequences

    I am currently working with the Phyloseq package in R to analyze 16s sequences. I sequenced the samples with Illumina's MiSeq platform.

    I want to see if I have pathogens in my samples and want to BLAST all the sequences from the Bacteroidetes OTUs but am having trouble figuring out how to determine which OTUs were bacteroidetes. Does anyone know the R commands for phyloseq that would allow me to do this so that I can go back to my QIIME outputs and get the sequences from those OTUs?
    Tags: blast, phyloseq, qiime
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