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454 data analysis in Qiime1

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  • 454 data analysis in Qiime1

    Hello
    I analysing 454 data using Qiime1. I have 4 .fna files that seem to be split into 2 forward read and 2 reverse read files. At what point in the pipeline should I combine them? Before demultiplexing? Combine the OTU tables?
    Thanks
    Laura

  • #2
    I don't know qiime well (only used enough to know that I strongly prefer mothur). So can't tell you exactly where to combine but you can't combine OTU tables if you do denovo clustering. In mothur, I combined after demultiplexing, sequence qc, and chimera checking but before aligning and clustering into OTUs
    Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.

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    • #3
      Ok thank you!

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